Bendis was suppose to reference it but had to cut it due to black vortex so blame Bendis on that X-Men tidbit. Everything else was referenced though.
I'm not sure I'd call the complete absence of any mention of the X-men declaring war on new york and the human race for a month a "tidbit". But let's continue-
There is a MASSIVE continuity problem with Avengers where Steve is Old and Sam is Cap now, but Steve seems to have forgotten he's declared war on the illuminati after returning from the future and finding out what they did. This is..not a small issue.
There's really no explanation as to how Cyclops ended up locked up in Genosha. This is problematic, since Cyclops and his team have been hidden so well not even SHIELD can find them, and boy have they been trying. There is also no mention anywhere during AXIS of Scott's team, which again is odd especially after undoing schism and unifying the x-teams. Apparently he "forgot" he had a massively overpowered team sitting on their asses in canada, at least one of which could have defeated Red Onslaught's sentinels single handedly by himself. (and speaking of those sentinels...where did all that adamantium come from? does it suddenly grow on trees? and why are sabretooth and carnage able to carve through it like tissue paper?)
Speaking of X-men teams, several of the All New X-men are inexplicably absent. Scott gets a pass for being in space with corsair. Bobby, Warren, and Hank are M.I.A. Jean shows up for 1 brief panel in AXIS #1, then vanishes, never to be seen again until the X-teams unify themselves after inversion in #4(?), then randomly hangs out being evil and inverted for the rest of the event. This is especially head scratching considering that quentin quire having to hold off Onslaught telepathically by himself (when jean should have been there) was a plot point. Things complicate further when considering that Jean and the O5 (minus scott) should have been in the ultimate universe at the time, and not in 616 at all!
AXIS Clearly takes place after superior spider man ends (as it's peter, and not ock) but after the avengers try to kill him, Spider Man flees with Nova and has "no one to turn to" as an ally outside of a handful of supervillains, despite Miguel O'hara and Silk both being active in new york at that time, and teaming with parker on a fairly regular basis. Nova has an entire team (the new warriors) he could call, but seems to have lost their number. Oh, and parker's clone is on THAT team, too. Keep in mind AXIS doesn't take place over 15 minutes, the manhattan takeover runs for at least 30 days. 30. Days.
On the X-men again, it's made clear that the inverted X-men are addressing at least SOME students who aren't inverted (as the dialogue makes clear, some of them weren't on the island and heard about it secondhand from quentin) and NO ONE seems upset at all that Apocalypse is apparently back, and 'war on the humans' is the new gameplan.
To top all of this off, the plan of the inverted Avengers was to kill the red skull so "no one could change them back because being evil is awesome!" The glaring problem here is that Strange's (where DID he go, anyway? why was no one concerned?) inversion spell, caused by wanda and doom (apparently) casting it wrong caused that. Everyone knows this because they came up with the plan in the first place. So why was the plan "kill the skull" and not "kill wanda?"
Speaking of Doom, there is a huge, complicated plot point where Doom ends up stealing some of wanda's powers though some kind of crazy machine he has laying around, and can use it to alter certain aspects of 616 history. Nearly anything he wants! After quite a bit of effort he decides to use this vast power to...bring back Cassie Lang? Ok. It's dumb, but we can accept this. she's a hottie. But a single issue later Doom brings back the VERY dead Brother Voodoo and Brother Voodoo's brother out of thin air, using the explanation of "oh, I know a guy, it's cool".
I could go on, but that would involve actually re-reading axis, and I'd rather not do that to myself a second time.