There is nothing wrong with the export. The Exporting of a C2 game will compact all the animations into a space efficient spritesheets for use in a C2 game. These sheets do not require the image sprites to be placedin order. C2 knows where the animation for what frame is and where.
C2 is not an art program, it is not sprite sheet editor, it is not an animation edit. It is a JS game tool kit. Which C2 does does fantastically well at.
Sounds like the problem was an expectation that C2 is an animation exporter which it isn't.