We have some reports with similar behaviour. E.g.:
I have also seen a thread where there is a description about sync issues particular with apple mail due to a wrongly implemented standard on their side.
Unfortunately, it is really hard to reproduce those issues and therefore hard to track down where the issue is and how to fix it. Any systematic issues that you see are highly appreciated for us to fix it. (Un)fortunately, I did not see any such problems on Ubuntu, Mac (both in productive use) or Windows (mainly for developing Mailspring fixes) so far and cannot help there for now.