He has just realised that an inmate has escaped on his watch, he’s probably in a world of trouble, I can see why his facial expression is a little bit shocked.
Valentine’s Day
If they get lucky, we’re all fucked.
He doesn’t look over at the bed, then approach the bed to make sure the dude isn’t asleep there. He looks at the bed then around the room and is sorta looking up, roughly in the direction of the poster when the scene ends. It’s not his shock, it’s the way he’s shocked. 
Possibly, but I think I’m actually confusing it with the Independence Day expanded universe novels. Yes they exist, and yes I read them.
But thats exactly the way somebody would look if there was nobody in the room?
Its a tiny room, he can see immediately that it is empty so of course he doesn’t go over to check the obviously empty bed, he doesn’t need to. He knows immediately the cell is empty and his face drops.
Star Wars prequels. People always claim that Anakin meets people in the Prequels who Vader shows no sign of knowing in the Originals.
Anakin/Vader only met the following in both trilogies, Palpatine, Obi Wan, Tarkin, Boba Fett and C3PO and he recognises all, except C3PO, with whom he shares only one scene: the Freezing Han scene where he is kind of preoccupied.
And there’s Protocol droids all over the place - heck, there was even a “rude” one on Bespin, so he should hardly be expected to recognize one he happened to build. I don’t go running up to every old Revell plastic model I see in a toy store and think it’s mine from 30 years ago.
Another from the prequels: Yoda is a great general in the prequels. In Empire, he dismisses the concept with, “Wars not make one great.” This isn’t an inconsistency, it’s character growth. It was his experiences during the war (which he lost) that made him realize the futility of war.
Well of course - the loser always says crap like that.
The miniaturized one in Tony’s chest seems to use-up the core material (palladium?). Presumably the larger one also does that. I don’t know how much a comparatively sized piece of palladium for the full sized reactor would be, but with palladium costing ~$800 a gram, I can’t imagine it would be cheap.
If they’ve plateaued, they’ve done so at a point far beyond where humans have currently reached.
Now sure,
IF they left enough information here for us to completely reverse-engineer their OS and
IF goldblum’s character was party to that information and
IF the aliens made a fundamentally insecure OS that can be completely brought down by a single virus and
IF their network infrastructure is also similar enough to ours that we can just plug regular laptops in via a USB to universe serial bus (see what I did there?) adapter and
IF they haven’t updated their OS in 50 odd years and
IF bringing down the OS literally brings down the ships
…then sure it “works”.
But if we’re going down that road, then no film has ever had a plot hole, since we can always make sense of anything given enough off-camera contrivances (just as we can defend any hypothesis in the real world given free rein to add whatever ad hoc speculation we like).
Though I agree with MaxTheVool that “plot hole” isn’t the term I’d use here. It’s just a weakness in the story that breaks any suspension of disbelief one may have (or it’s possible to have watching a sci fi).
It’s palladium until late in the second movie (I watched the whole trilogy yesterday and the day before), yes. He finds a less toxic replacement later on, but probably not a more cost effective one.
Another Star Wars one. The port hole was no undefended, it was actually ray shielded.