If anyone can tell me how and when the Autobots got captured, then I'll tell them how Meggy got in the alley to sulk.

 

I'm pretty sure 'Bee was dealing some whippets and goofballs to the rest on the street corner, for a quick rush during the battle. Barricade of course caught wind of this and took them in for some questioning and/or death.

 

He fell down some stairs.

 

Megatron was in the alley because he was told there'd be punch and pie.

They tripped over a bit of jutting-out plothole?

 

*trip* "Gosh darn it, Mike! We told you and the construction crew to fix that!"

 

Help - I've fallen into a plot hole and I can't get up!

The construction crew were gonna go put some plating over the exhaust port on the Death Star but that can wait until later while they plaster over the Autobot capture hole. I doubt a small bit of exposed exhaust port will be much of a problem anyway...

 

I always thought he fell down when Optimus shot down the control pillar.

 

Either this, or he merely slipped away while no one was looking (after Sentinel hopped down to confront Optimus). He probably needed to spend some time alone so the Doctors could do their work.

(Keep in mind, he only swats the Doctors away when someone else is in his presence (especially someone like Starscream), fearing that it'll give the impression that he's weak and powerless, possibly leading to him losing his control over the Decepticons and/or his assassination.)

 

Megatron can now drive down the sides of buildings! It's a Fact!

 

I'd say a more mysterious question would be: How did Sam get to Dylan's mansion?

 

He probably just walked to the alley