How to tell where emails are being deleted from?

I've been running into a recurring issue with Gmail where emails are inexplicably deleted, and I can't figure out why. Most of my emails get to my inbox fine (and stay there), but occasionally emails will end up in the trash.

For example, I'll be working on my computer and

1. My phone (iPhone) lights up with a lock screen notification showing email(s) arrived
2. I open a tab to Gmail on my computer and by the time I've gotten there one or more emails have been deleted.
3. There doesn't appear to be any patte to which emails are deleted, and it only seems to happen occasionally

The only reason this conces me is that third point, I could miss something important if I don't see a notification for it. Has anyone had issues like this, and are there any ways of seeing how emails are being deleted?

Note that I have no filters on Gmail. I use mail applications on iOS and OS X (also no filters or rules). I used to use Unrollme but have long since disabled it.

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