Im pretty sure I've found a bug with texture packer, if i use a image twice in a skeleton under two different bones, then texture packer gives warning name of texture has already been packed. Additionally first time you do this with warning you will get name.atlas + name.png, next time name.atlas + name.png + name1.png then name.atlas + name.png + name1.png + name2.png and so on...

There shouldn't be anything blocking spine deleting the files apart from spine itself. Im been suffering lately a lot of similar problems. Also appears it can happen on first export.

btw should say I've been experiencing issue on OSX version.