In MIssion 2-2 there are 48 kills in total according to the ending screen. However, I've only managed to find 47 enemies on the map despite hours of replaying.
After having watched another video playthrough, I've come to the conclusion that there's one of the yellow ninja guys that just do not spawn for me. It' s the one on the top walkway of the first building after the first "scene change", i.e. right after going in the door following the bridge with GLOPP under it.
It might be that this is an enemy that can spawn in several spots, but I doubt it. I've counted no difference in the number of enemies encountered by me and by the video I've been watching before or after that spot. I can't find that extra enemy anywhere. And yes, I've stomped the crocodile and all the rats.