Some emails get captured while some that I’ve flagged don’t, is this a bug?

Probably not. We have explained this in length in this article, we’d highly recommend you give it a full read, especially the How Capturing Works and What Gets Captured sections.

There’s also a big gotcha - if you have setup the same account (as it has been advised against in the article linked above), and then have the Unset Flag option turned ON for that account on either device, your two devices may compete with each other and the first one to capture it will unflag it. This will then make the second device ’miss out’ on the particular email. You should eventually have the emails synced through when the other device syncs, but this may lead to confusion. For this reason amongst others, we advise linking a single email with a single device.

Please also note, some email clients also seem to be setting the Important header option ON for emails that you flag (which, strictly speaking, are not Flagged emails) and this may also be why 2Do is unable to capture them. Please try switching the Marked as Important option ON under Settings > Email to 2Do > Account > Capturing Rules and see if this helps. 
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