I ran into almost the same problem. Luckily I didn't increment the major number, but only the minor. However, since we're an Open Source project of course the major is "0" (though we are considering going to 1.0.0 - maybe next year), and thus our minor also had to increase (from 0.9.x to 0.10.0). Since then I really take care to check the version and build numbers before submitting to Testflight...
Topic:
App Store Distribution & Marketing
SubTopic:
General
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