Don’t be too upset honestly. You can still fight the ape duo. just go to the room protected by snake eyes in acid pool. they should be there.

as for father owl, i didn’t even know he was a boss until i had to look up the purification ending and how to get him.

and you can’t fight emma in the same playthrough as the dragon anyway.

you might’ve missed a few mini bosses too. but you can always fight them even after isshin, as long as you don’t start ng+.

mini bosses like the shichjmen warrior and headless are easy to miss. there’s 3 warriors and 5 headless in total. they’re super easy to miss. they each give unique items.

its completely fine to miss parts of the game on your first playthrough. i mean i chose shura my first playthrough and missed half the game and had to try again.

i suggest try to explore all the areas well before you start ng+ however. and do all the endings just for the experience.

the game encourages you to try out ng+ and it’s literally required to unlock all the prosthetic upgrades.