Do you have specific examples? I've only heard of a small amount of things that are not flagged correctly (for instance Conrad Verner saying you pointed a gun at him in the conversation with him in ME2 regardless of what you did in ME1) and have never been corrected, but nothing major. You could always try Gibbed Save Editior, the flags usually have a short description so that you know what they are for.
off the top of my head:
-On the last mission of Omega, When entering Gozu, Aria Doesn't bring up mordin
-Kenneth and Gabby's argument near the end of the game
there might be others, i haven't kept track of all.
Also, the ME1 data for verner(hossle, asari writings, license) works
I tried using Gibbed to take the working career and change the gender and relavent flags. didn't work, plus it might be bad for the code (however no apparent effects, except some slows in the shepard's squad screen)
I think Aria mentioning Mordin will most likely be triggered by events in ME3 themselves, like if you've done Tuchanka already and the different results there. Ken and Gabby was afaik bugged and you didn't hear banter from them if you had Kaidan as squadmate instead of Ashley, but I thought they fixed it with the Extended Cut. Maybe the didn't fix everything. But certain Ken and Gabby scenes only trigger if endorsed, like the scene beneath engineering, where Jack "lived" in ME2.
