Hey!
Did you manage to upload since you posted?
I experience the same issue with some other issues, when I manage to upload from xCode, I get later an email saying ITMS-90338: Non-public API usage, but after a through investigation, I couldn't find anything wrong.
Also when I tried to re-upload the same code that is already in stores with a different version number got the same problem.
Created a ticket for apple but no way to escalate or get a quick response yet.