S01E01: red skull doesnt find the tesseract until after peggy undergoes the experiment and becomes captain carter, in the main timeline red skull finds the tesseract in march 1942, over a year before steve undergoes the experiment himself
S01E03: hanks motivation for killing the avengers is the death of hope working for shield two years prior to furys big week, meaning the point of difference cant be tony dying in the donut shop
S01E04: not so much an "issue" but how can christines death be an absolute point if it doesnt occur in the main timeline?
S01E08: theres no way for thanos to have collected the remaining five stones by 2015, and if he did it had nothing to do with ultrons success on earth (im willing to explain this away by saying it had been 3 years and by 2018 thanos was on the infinity conquest but that causes more issues later in the episode); if we assume the episode is in 2015 then ego would have already been killed, and if we use the 2018 explanation then asgard would have already been destroyed as well
S01E09: in the universe where uatu leaves the black widow variant loki shouldnt have his staff as he ruled earth before having met thanos to get it from
S02E01: yon-rogg, korg, miek, and drax all being on xandar in 2014 aren't necessarily accurate, yon-rogg is a possibility as we dont know anything about his fate since june 1995 in the main timeline
S02E02: if the episode takes place in june 1988 and quill was abducted 6 months prior that would make it december 1979, which would have been earlier than the main timeline; also hank doesnt leave shield until 1989 in the main timeline while here he had by june 1988
S02E03: the other avengers shouldnt yet know about clints life outside of being an avenger
S02E04: tony has the armor from iron man 3 that comes to him in individual pieces which he hadnt invented in the original avengers
S02E07: hela is banished to hel before the year 965 and wenwu doesnt find the ten rings until around 990-1000 in the main timeline, meaning he found the rings earlier here
S02E08: the appearance of the freak here suggests that things are slightly different in the universe where the characters come from, however even if everything except for the freaks appearance occurred exactly as in the main timeline hela and the destroyer would have been dead before 2018