This happened to me a few times already, before the latest additions as well as before them. In short, I enter the zone afresh and not evne crates spawn in their usual places, let alone presents or named bosses. Exiting and re-entering right away doesn't fix it, either. I have to take at least five minutes break before re-entering again for everything to start working properly. Sometimes, it even takes me two tries (exit -> wait five minutes -> enter again) to get everything to work.

This is intended, all spawn timers reset when you exit a zone, however it's only for that particular zone. So you can exit one zone, go hang out in a different zone for awhile and then exit that second one, and the first zones spawn timers will not be reset.