idk, her fear being the Doctor seemed pretty easy to me - why would she be afraid of the suit eating her, if she was already in it and using it to call the White House? And the fact she bolted when he showed up despite calling for help, which everyone else seemed to think were plot holes. I just hadn't thought about how growing up with that fear of him might affect her as an adult, but now you've explained it it seems really obvious.

Fear = chaos is also a thing in AGMGTW- Colonel Manton tries to talk up the soldiers and tell them the Doctor is just some dude they'll defeat easily, but then he appears, and they freak and start shooting into the Monks. And during River's verbal spanking later on she makes the point that it's about fear - "you make them so afraid." "all this ... in fear of you." Doubtless, if they're doing this out of fear, that's what they're going to brainwash Melody with.

So I don't think it's a hole, really, we just have to go looking for all the pieces, and there's so much STUFF in these episodes that it's easy to overlook stuff.