1) The actual plot of Mass Effect 3 supposedly takes place over several months, people. If the crew was being indoctrinated, even if it was slow and gradual, it would have completed itself well in time before Shepard's charge.
2) Someone being "fully indoctrinated" would be the equivalent of a Collector. TIM and kai Leng were hardly any such thing but they were still firmly in the grip of indoctrination, akin to Saren. As the Prothean VI ran away in the presence of Kai Leng, it's safe to assume it can detect the gray area in between "full" and "not".
3) Javik, you know, being special, should've likely been able to both recognize and tell whether or not people were being indoctrinated, even if it was gradual. He could pick up on Miranda, from 6 months ago, and her genetic code to the degree that he could even tell she was artifical. He could tell the exact thoughts of Grunt. It's entirely reasonable he could've detected indoctrination; especially since he was on edge and looking to fight the reapers entirely and didn't trust the crew at all.
4) Joker was on the Normandy SR-2 the entire time of Mass Effect 2 (and likely before as well), during the 6-month gap between games, and the entirety of Mass Effect 3 as well, which should add up to at least a year, if not closer to two, and he showed not one sign of it at all. He even personally bombed the reaper (unkowingly admittedly) on Rannoch and (according to deleted audio) was supposed to lead a strike force to kill Harbinger itself.
5) Asari, explicitly, have been able to tell whether or not they are indoctrinated through the example of...Rila (I think). She said it was already too late for her and she wasn't physically harmed at all. The Shadow Broker, also being an asari, should've also had that same self-awareness. Especially since I'd bet a Black Widow on the fact that Liara is a sight more experienced with indoctrination and the Reapers than an Ardat-Yakshi who's lived in seclusion for centuries.
6) If the Prothean-made, entirely secret Mass relay on the Citadel makes you hear humming as if you're being indoctrinated, then something is really really off.
6a) If the statue in the Citadel could indoctrinate you then, frankly, the entirety of the Council should've been indoctrinated, as well as most embassy staff, and everyne who worked on the upper Presidium, including that Asari hooker. That's just being conservative.
So we have the least interesting character of the entire game, thrown in there to be the vessel of the "common man" saying one thing sounds weird in the shuttle bay (note: not engineering) and some throw-away line from kaiden, who admitted his implants gave him things like headaches, ringing in the ears, bouts of nausea, and just overall crappiness, and "humming" being a common noise in indoctrination.
....You're grasping at straws, people. At least Tali had the excuse of being entirely drunk (for likely the first time) before she started trying to make it sound cool.