More ROTF Questions?????

Okay, every time I watched this movie, more questions pop into my head.
How the hell did Wheelie get into Bumble Bee's trunk.
Sam grabbed the bin w/Wheelie when they were running from the pretender.
They were then airlifted by Grindor and dropped into the warehouse. Starscream then sawed the car in half. In running from missiles and explosions, who had time to grab the metal container with Wheelie??
Why was the military commander not allowed to see Optimus but could only hear him speak? After all he saw Blackout and scorp' in the first movie wipe out an entire military base..
And also, why the hell were the Autobots taking orders from the US Military in the run up to the final battle?
I'm not here to start Michael Bay attack fest, just wondering if anyone has any possible explanations.
How the hell did Wheelie get into Bumble Bee's trunk.
Sam grabbed the bin w/Wheelie when they were running from the pretender.
They were then airlifted by Grindor and dropped into the warehouse. Starscream then sawed the car in half. In running from missiles and explosions, who had time to grab the metal container with Wheelie??
Why was the military commander not allowed to see Optimus but could only hear him speak? After all he saw Blackout and scorp' in the first movie wipe out an entire military base..
And also, why the hell were the Autobots taking orders from the US Military in the run up to the final battle?
I'm not here to start Michael Bay attack fest, just wondering if anyone has any possible explanations.