Not sure what you mean by different sizes. All spritesheets can be dividided evenly into 128x128 cells. All enemies fit well next to each other as well and other of my packs as well.
I would be interested in the game engine you are using? Other developers haven't had any issues with the assets so I'm intrigued.
But for most game engines the workflow is quite simple, slice, set each cell to 128x128, drag into animations and done.
That being said, I'm glad you like the art