Oh, this is gonna be sweet:
Cipher never being truly explored
inconsistent description of the genophage
Bizarre quarian immune system
SR1 getting blown up and Shepard spaced in the opening moments of ME2 leading to...
The Lazarus Project
Cerberus being whatever sort of organization Bioware needs it to be at a given moment
Shepard being TIM's b*tch for 99.9% of ME2
Horizon in ME2 and the stupidly OOC behavior if both the VS and Shepard
The entire central plot of ME2.
Han'Gerrel going full-on General Ripper for ME3 when he was a pretty reasonable guy in ME2.
"the essence of a species"
"organic energy"
spandex/stripperific armor
Why ME3 didn't open with a "Critical Mission Failure" given how powerful and numerous and (supposedly) smart the Reapers are.
Ashley's makeover in ME3
Ashley having virtually nothing to say in the second half of ME3
Ashley's personality transplant in ME3
Ash's discussion with Shepard about the afterlife being cut from ME3
The Catalyst being an AI on the CItadel this whole time
EDI's sexbot appearance
Priority: Earth
Citadel: The Return
RGB
I'm sure there's more. THis is just off the top of my head