It's kinda weird because there was a vague reference to the Infinity War last season, but nothing since then. Instead, we've gotten a few references to time travel and how going back and messing with the past will create alternate timelines, which are each completely valid alternate realities and, best of all, you don't know which one you're in.
I kinda took that as their explanation for why Agents of SHIELD isn't in sync with the MCU any more, but mostly I just don't let it bother me because we know the constraints they (the writers) were working with, and their solution is good enough.