Cordova: Unexpected Machine Code - Your upload contains both bitcode and native machine code
Posting an answer myself, as it seems to be quite a popular question with nobody answering — so the issue is on the Apple side. Some people contacted Apple support and confirmed this. There is no need to recompile anything. The binary with such a warning can be submitted to the AppStore — it will pass the review successfully. I've already did it with a few apps.
Check more details here: "Unexpected Machine Code" warning from iTunes Connect
I've found this thread:
https://forums.developer.apple.com/thread/50328
suggesting to set Enable Bitcode to NO but in my case it already was on NO and still got this message... :-\
however, another guy said:
"It's happening to me as well. On stack overflow someone's says they called iTC and it's a problem on their side."
so I hope it has no effect, and it'll gone as it appeared...
I also got the same mail and, it's a bug, 
Check this answer https://stackoverflow.com/a/38061592/3626659