Played the Ex-Cerberus Scientists mission a lot today, here's a couple of things I noticed for the first time:
-EDI is the only one from the ME2 crew that Jacob doesn't recognize (obviously), and EDI comments on that. She says that Jacob didn't recognize her and that it might be time for a surprise. Shepard is a killjoy and tells her to focus on the mission. Aw man.
-When skipping some dialogue with Brynn after getting inside, I had a brief glitch where the squad mates want to go downstairs instead of following Brynn and Shepard. Didn't happen all the time though.
-You can take out the Shield Pylon when going up the ladder to fix the satellite with powers (either your own or your squad mates). The 2 Cerberus mooks standing next to it won't react to that even when you do that multiple times 
-The Cerberus Engineer in front of the satellite tower is called Thompson (one of the Cerberus mooks you fight earlier in this area mentions his name).
-If you leave the Cerberus trooper on the gun on the roof he will be gone automatically when going up the ladder.
-During the AA gun section, the sentence of FemShep asking how progress with the gun repair is is bugged. Even when subtitles are off, the subtitle will be displayed, but there's never any audio.
-Theoretically you can stay in the shuttle bay at the end and fight from there, even the Atlas. Only when you go outside will it be closed and you can't re-enter. But hiding like that is no fun, right? 
-If this mission is played after Rannoch, the pissing contest Garrus and James have on the Crew Deck will change slightly, depending on what happened on Rannoch. When they talk about how great they are when teaming up, Garrus mentions it if peace was made, and if the geth got wiped out. If the quarians died Garrus refers to stopping Cerberus on the Citadel instead.