I might be a "Gmail is weird" issue but I've always had trouble going through my inbox and deleting a lot of email one by one. They disappear, then they come back and then disappear again. Hitting undo after deleting something by mistake is also a recipe for disaster for email that kind of disappears but still shows up in search.

It can also be pretty laggy (e.g. selecting multiple messages), but this has gotten a lot better in High Sierra.

I still use it though since I have yet to find an alternative that I prefer (I've only tried a few though)