In the end we see that the Collector General is released from his Assumed Direct Control that Harbinger had over him when the Collector Base is destroyed, implying that throughout the game the Collector General was being directly controlled by Harbinger.
But wouldn't this mean that whenever Harbinger yells "ASSUMING DIRECT CONTROL" and takes over a Collector Soldier, that he releases his hold on the Collector General while he does this?
Direct control is not exclusive to the Collectors, but seems to require direct modification of the subject to work. Direct control may strengthen the subject but is potentially very taxing on the Reaper performing it if the subject dies or is destroyed at the wrong moment.
SAREN: You survived our encounter on Virmire. But I've changed since then. Improved. Sovereign has... upgraded me.
SHEPARD: You let Sovereign implant you? Are you insane?[Nearly all of Shepard's lines in this and every cutscene prior to ME3 are chosen by the player from multiple options. Cutscenes may differ substantially depending on those choices.]
[SAREN talks about how SOVEREIGN brainwashed him with the implants and gives a generic "you could join us" appeal, SHEPARD argues with him, etc. Skip to 2:18.]
SHEPARD: Some part of you must still realize this is wrong. You can fight this!
SAREN: Maybe you're right. Maybe there is still a chance for... unh! The implants... Sovereign is too strong. I'm sorry, it's too late for me.
SHEPARD: (Gets out of cover.) It's not over yet. You can still redeem yourself!
SAREN: Goodbye, Shepard. Thank you. (Shoots himself in the head.)[Various plot-related things happen. Skip to 5:42]
SHEPARD: (Looking down at SAREN's body.) Make sure he's dead. [Voice line is female because the user modded the game, but the mod does not otherwise affect this scene.]
GARRUS and KAIDAN (or whoever happens to be present instead of them) climb down into the garden where the body fell. GARRUS shoots SAREN in the head again.
KAIDAN: He's dead.
SOVEREIGN, who is latched onto the Citadel Tower just outside, takes control of Saren's body with an effect somewhat similar to that of HARBINGER, but more physical. The body is significantly altered. Limbs grow longer and less humanoid, implants are exposed, and a small amount of flesh is left clinging to them.[Boss battle, and a brief plot-related interlude. Skip to 9:31.]
SAREN's body is destroyed. The resulting feedback courses over SOVEREIGN's body. SOVEREIGN releases its hold on the Citadel Tower.
JOKER: Its shields are down! Now's our chance!
HACKETT: Hit it with everything we've got!
The ENTIRE ALLIANCE FLEET starts firing on SOVEREIGN. The NORMANDY pulls a U-turn.
JOKER: Hard on my flank! We're going in!
The NORMANDY and the FLEET both continue firing. They blow a hole in SOVEREIGN and it begins to break up.
It's fairly obvious that it would have been much harder, if even possible, for the Alliance fleet to destroy Sovereign if it had not tried to take control of Saren's body.
The Collectors were genetically modified by the Reapers, so that direct control was possible but normally unnecessary.
Transcript:
EDI: [...] only one race is known to have this [genetic] structure: the Protheans.
SHEPARD: I thought the Protheans vanished 50,000 years ago. I can't believe the species still exists.
EDI: These are no longer Protheans, Shepard. Their genes show distinct signs of extensive genetic rewrite. The Reapers have repurposed them to suit their needs.[Skip to 4:25.]
EDI: This Collector likely descends from a Prothean colony in the Styx Theta cluster. But there are signs of extreme alteration. Three fewer chromosomes. Reduced heterochromatin structure. Elimination of superfluous junk sequences.
SHEPARD: I wouldn't want to live as some kind of mutated slave. Killing a Collector is probably doing it a favor.
Finally, there is no canon evidence from any of the games that a single Reaper can control multiple subjects at once. In Mass Effect 2, there is only ever a single Harbinger-controlled Collector on the battlefield at any given time, and there is (depending on difficulty level) normally a "cooldown" period between these appearing. This suggests that Harbinger is feeling the full brunt of the backlash every time Shepard kills a possessed Collector, which prevents it from taking control of a second Collector until it has recovered.
Putting all of this together:
An alternative theory, which I've heard but have seen no evidence to support, is that Harbinger is only ever controlling the Collector General, and the General is then controlling the footsoldiers on behalf of Harbinger, in order to avoid the backlash problem. The difficulty with this is that there is no evidence that the Collector General can do that. Sure, the Collectors are insectoid, but Javik shows no evidence of being able to control other Protheans in his flashback scenes, so it would have to be a capability which the Reapers added. However, the Reapers were removing things, not adding them. I find this theory interesting but unpersuasive, and include it for completeness.
We don't really know, but since all Collectors have been fully indoctrinated, there are only two options:
There's no evidence Harbinger exerted direct control over individual Collectors as a routine matter. It's only when Shepard, who has already been demonstrated to be a pain in the ass to the Reapers, shows up (after being dead) that there's evidence of Harbinger doing it. Prior to that, Harbinger might have simply possessed a Collector (including the General) from time to time just to keep tabs on what was happening. So General(s) might be used to Harbinger popping in and out from time to time.
The General freaked out in the endgame not necessarily because Harbinger stopped possessing it, but because Harbinger was abandoning them.
