Never found a list like this, so decided to make my own. Here we go! Not going to be including the requirements of the fights for maximum Karma. This list is mostly useful in the later chapters that have a ton of hidden fights that are way out there somewhere and require some backtracking. If a fight can be easily missed, i'll note as such at the end in bold.
This list is a work in progress.
CHAPTER 1 - "The Way of the Ninja"
Chapter 2 - "The Hayabusa Ninja Village"
Chapter 3 - "Skies of Vengeance"
Chapter 4 - "Imperial City Infiltration"
Chapter 5 - "The City of Fiends"
Chapter 6 - "The Monastery"
Chapter 7 - "Hidden Underground"
Chapter 8 -"Tairon Under Alert"
This list is a work in progress.
CHAPTER 1 - "The Way of the Ninja"
- Go up the hill and you'll activate a cutscene, can't miss it;
- Go further up and you'll enter a cave, can't miss it;
- Wallrun up and watch the cutscene, two ninjas will jump in by the torches, can't miss it;
- Go further in, open the door. Be careful not to open the door by accident, or you'll void this fight;
- Open the door after this to be ambushed from above, can't miss it;
- Go into the room with the statue, turn the corner, hard to miss;
- The room after this is a big open space with weapons being displayed, can't miss it;
- The Ambush Room after this contains one ranked fight, be careful not to fall down, missable;
- Drop down after the Ambush Room, hard to miss and short fight;
- Go further up after the cave and you'll be outside the complex. You'll fight two ninjas here, can't miss it;
- Go straight ahead after the Save Point to encounter two more ninjas, can't miss it;
- Use the key to open the door, you'll get one big fight, can't miss it;
- Open the final door and face Murai, can't miss it.
Chapter 2 - "The Hayabusa Ninja Village"
- While trying to leave the fortress at the start, you'll enter a yellow room where the door locked for an ambush in Chapter 1. Wait here for a bit and you'll trigger another one, missable;
- At the Altar right before getting the Fire Wheel Ninpo you'll be ambushed, hard to miss;
- Continue along the way, open a chest that contains Smoke Bombs and you'll encounter some samurai, hard to miss;
- After sliding down a mountain you'll be ambushed again, careful not to fall in the water or you might void the fight, missable.
- Enter the village and after a cutscene you'll be rushed, hard to miss;
- After getting the bow exit the building normally and you'll get one last regular encounter, can't miss it;
- The horse fight, can't miss it;
- The final boss fight of this chapter, can't miss it.
Chapter 3 - "Skies of Vengeance"
- Enter the room with the map, fight triggers after this, can't miss it;
- Go to the main hallway afterwards for a forced fight with some soldiers, can't miss it;
- Enter the Crew Compartments for a forced fight, can't miss it;
- Leave the Crew Compartments to the next hallway, and re-enter the Crew Compartments and re-enter the hallway again. It will spawn a short fight with some soldiers. Missable;
- Go down the elevator for a forced fight, can't miss it;
- Straight after this fight an elevator will come down with another forced fight, can't miss it;
- After the save point you'll have to turn a crank, half way through you'll be ambushed, can't miss it;
- Once the crank is turned, you'll get a short ranged fight, can't miss it;
- Before crossing the rope, backtrack to the savepoint and enter the door to its right (while facing it), you'll get a short hidden fight. Missable;
- Once you cross the rope you'll get a short fight, careful not to fall of! Can't miss it;
- Once you enter the back-deck you'll have to walk up some stairs while being fired upon, can't miss it;
- Further on you'll get another fight, hard to miss;
- At the Save Point before Dynamo you'll encounter some foes, can't miss 'em;
- Dynamo lies in wait at the end, murder him! Can't miss it.
Chapter 4 - "Imperial City Infiltration"
- Right after the Save Point, can't miss it;
- Right after the Serpant Statue head left to the big open area, you'll encounter some soldiers, can't miss it;
- Big area with mounted guns, can't miss it;
- Right after this fight enter the door with the orange-dot, you'll encounter another short fight. Can't miss it;
- In the big plaza after this (with the rope up top) you'll have a short ranged fight. Note that if you don't look at them, this fight won't trigger. Can't miss it;
- Enter the Yellow Door and try to continue, the doors will lock and you'll get a forced fight. Can't miss it;
- Go up through the blue-mini door in that area for a small fight, missable;
- Going further up you'll encounter some ninjas, just before the Spirit of the Devils. Missable;
- Continueing on you'll enter a place with a caged of area and a destructable wall. Enter the caged of area for a hidden fight. Missable;
- In the same area continue the way you're supposed to for a few ninjas to fight, can't be missed;
- Once you return to the plaza where the shop is, you'll get another small fight. Can't be missed;
- Backtracking towards the locked door in the plaza with the rope, you'll find two soldiers up top. Missable;
- Returning to the area with the breakable wall, you'll find some more ninjas. Missable;
- Enter the Pleasure District to kill off some ninjas, can't be missed;
Chapter 5 - "The City of Fiends"
- Drop down the ladder, fight is right around the corner. Hard to miss;
- Further along inside the building you'll encounter some more ninjas, hard to miss;
- Outside the bar there'll be some soldiers waiting for you, can't be missed;
- After using the Lily Key you'll enter the next room and fight some dudes, can't be missed;
- On the Moat Road further up you'll encounter some ninjas, can't be missed;
- Go through the red door after the Save Point to spawn a few ninjas, missable;
- At the Save Point go up the stairs to the Drawbridge Square and fight the soldiers, can't be missed;
- Enter the door after the fight and you'll spot some enemies further across, hard to miss;
- After crossing the bridge you'll find a Save Point, just before it you'll be ambushed, can't be missed;
- Afterwards enter the Monestary Plaza for a forced fight, can't be missed;
- Afterwards continue on as normal to be ambushed by ninjas, can't be missed;
- Few steps further and you'll be ambushed again by ninjas, can't be missed;
- At the end you'll fight some soldiers, can't be missed;
- After that you'll fight some Gala, can't be missed;
- And after that the boss, can't be missed;
Chapter 6 - "The Monastery"
- Backtrack at the start and go up the stairs for a hidden fight, missable;
- Once you reach the courtyard of the Monastery you'll encounter some cats, can't be missed;
- Go through the big door at the Save Point to the Monastery Plaza for another hidden fight. Missable;
- Enter the Monastery and walk to the center of the room for a fight with the monks, missable;
- Once you continue on you'll get a forced fight with Fiend Ryu, can't be missed;
- After that fight you'll have to break a wall, you'll get a fight behind it, can't be missed;
- After you pick up the Book of Eons you'll be ambushed, can't be missed;
- Drop down to the central plaza again for another round against some Monks and Bast Fiends, can't be missed;
- Return to the Archives where you fought Fiend Ryu for a Fiend Challenge, missable but you can revisit this fight for nearly the whole game;
- Drop down where you're going to offer the sacrifice later, you'll spawn some imps, can't be missed;
- Further along you'll encounter a fight with some bugs, can't be missed;
- Eventually you'll enter a room with a big chain at the center, you'll encounter some imps here, can't be missed;
- Take the elevator down as planned to encounter some more imps, can't be missed;
- Go deeper in and you'll encounter more bugs in a small room, murder them, can't miss it;
- Afterwards you'll encounter some bigger zombies, can't be missed;
- Exit the room to head back to the elevator for another fight, hard to miss;
- Ride the elevator back up again for another fight, can't miss it;
- The room with the chain also has some zombies now, can't miss it;
- Walk up and you'll encounter some archers, can't miss it;
- Before the end of the chapter you'll fight the Bone Dragon, can't miss it.
Chapter 7 - "Hidden Underground"
- Instead of continuing on, head back to the elevator and go to the room that held the chalice. Along the wall you'll get a fight, missable;
- Inside the room with the chalice is a Fiend Challenge, missable;
- Going back to the way you're supposed to go, after dropping down enter the door with the Egyptian symbol on it to be greeted by a few archers. Can't be missed;
- Drop down the bridge and fight the gauntlet, can't be missed;
- Enter the Blue Door and fight the archers, can't be missed;
- Leave the room again to the main room and be greeted by yet another fight, can't be missed;
- Go through the Red Door and fight the archers, can't be missed;
- Hydracubis fight, can't be missed;
- Go up the wall and grab the Jewel of the Demon Seal, three archers will spawn, missable;
- Go down the hallway and fight some archers and regular zombies, can't be missed;
- Further along you'll encounter some Ghost Fish, kill them all, can't be missed;
- After that go through the door and fight some more Ghost Fish, can't be missed;
- After the flood, go into the elevator below and fight the cats, can't be missed;
- Alma fight, good luck, can't be missed.
Chapter 8 -"Tairon Under Alert"
- Return to where you fought Hydrabuscus for a hidden fight with some soldiers, missable;
- Enter the Monastry Plaza for a forced fight, can't be missed;
- Go up the stairs for another fight, can be missed if you go the wrong way;
- Cross the bridge to fight a few soldiers and a tank, can't be missed;
- Continue along the way to a cracked wall where you'll get a short fight, can't be missed;
- Backtrack to the Lily Door, there's a hidden fight on the staircase there. Missable;
- Backtrack further to the Clock Tower Plaza for a fight against a tank with some soldiers, near Murasama's shop. Missable;
- Go further along to where you'll get the Dabilahro for the hidden fight against two Berserkers. Missable;
- Backtrack to the tunnel where you use the Pegasus Key for another hidden fight. Missable;
- Go back to Han's Bar for another fight, missable;
- Just before you reach the skull door you'll be ambushed while going up the stairs. Can't be missed;
- Backtrack a bit to the Entrance to Tairon where the save-station is for another fight, missable;
- Right before entering the big door for the big fight you'll get a small fight with 3 soldiers, can't be missed;
- The big fight at the gate, can't be missed.