I just finished a rewatch of AoS and part of the last season was on an alternate Earth, but they made it clear that they returned to the prime timeline that all of the MCU stuff takes place in. And they had Graviton ready to attack Thanos before the events of Infinity War. It was all within canon events, just a lot of the average viewers didn't understand that.

All of Agent Carter took place directly after the events of Captain America: The First Avenger and after the nod in Endgame should be in canon.