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If I export my game as iOS IPA from AppGameKit and set version number to "1.0" and build to "60", the game when uploaded to iTunes Connect will have version number 60.

If I set version number to "1.0.1" and build number to "60", it will upload as version "1.0.1".

If I rename the produced .ipa file to .zip, extract and look into the .plist file, it shows that the CFBundleShortVersionString key is actually set to 60 for the 1.0 version and to 1.0.1 for the 1.0.1 version. So the problem seems to be in exporting with some specific version strings.

This also created a version number in iTunes Connect with a big number. So the 60 version is now always higher on the list than any other. Does anyone know of a way to delete such builds? The iTunes Connect UI is not very intuitive for me.

Thanks, fixed for the next version. Unfortunately I don't know if there is a way to set the version number back, although if you haven't yet submitted the version I imagine it should be possible. If not you may have to ask Apple to change it.