That is pretty normal if you’re still using v2 in AnkiDroid – The Anki v3 scheduler - Frequently Asked Questions . I don’t think it’s a sign they’re out of sync.
I’d recommend enabling v3 on AnkiDroid though (directions on linked page). I’ve been using it in 2.16.5 for over 6m with no issues.
(No idea if it will help clear the pop-up issue.)