These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Fridge Logic: OVER-1 is said to be a new Reploid in the storyline, but the definition of a Reploid according to Mega Man X is any androidreplicated from X's original design. Does this mean this takes place after X was sealed away by Dr. Light? Also, if we're to take Maverick Hunter X as canon, Light seems to be on the verge of death after completing X if that's the case.
Compounding this, the Mega Men that Over-1 set out to rescue? Completely absent (not counting Battle Memory and that one set of armour). And on top of that, all the series are kept as rigidly separate as possible, with only a single connecting element (Over-1) to indicate that there's a crossover going on at all.
Possibly taken Up to Eleven when three fan developers managed to create the Rockman Xover demo, in under 24 hours. Comparing the fan game to the actual game's footage, they're almost completely identical.
The final game is just as tedious as all prior evidence suggested—and it's fairly glitchy, to boot. The first stage/section doesn't even have any real enemy variety.
According to one person who played the game, there's a limited music and enemy selection, a good deal of the bosses are from X1note leading to the implications that Capcom was too lazy to add any other bosses, and simply reused the sprites they had, and Over-1's running animation "doesn't even go past 7 frames and looks choppy."