Just throwing it out there, but the scene would've read much better if they'd decided not to start with a telepathic contact/intrusion just in case the-boy-with-an-island freaked out over it. Chalk up the subsequent post-Nathan-screw-up delay to the stress of battle and there you go. Oh well.
Still, after that whole 'Hey, turns out those Krakoan security scans were worthless since day one, lol' insanity, just about any other sketchy plot point/straight up plot hole feels like really, really, really small potatoes.