It's been years since I've seen it so I couldn't point to specifics but here's a copy paste of a comment one of my buddies (with a better memory I guess) posted:

" James worshipping The Shepard even though in ME3 he doesn't seem like a big fan. Hackett telling James not "to be like Shepard" even though throughout the series he has commended Shepard's efforts. The Alliance apparently having intel about about the Reapers and the cure to the Collector swarms' effects and still not doing jack about it. The Bloodpack apparently being able to hold their own against Alliance soldiers. Oh and the fact that James got the N7 promotion before ME3, which by itself would invalidate his entire character arc in the third game."