Every time I upload a new version I delete all files and then upload new ones.
Because newer version may have differently organized sprite sheets, I guess, while naming remains the same, you may get cached files shown instead of new ones and they don't fit the newly exported version.
Basically you have something like shared sheet 0 in your export, but now it contains different images, so it looks like nonsense.
This happens even when not dealing with cached files. I guess game code may point to images on that sprite sheet and if you only upload new script files ( after a minor change ), or try to rewrite files, they still may come out wrong.
Therefore nuke everything, then upload a new version.
Not much you can do for people who already have the game and get served rong cached files ( other than tell them to empty their cache )