Again, don't need everything to be "officially answered", but to speculate a Darkside (somehow commanded by Xehanort?) picked up Aqua and tangible Not!Ven(?) and then (I can only assume) casually dropped them off / Mickey rescued her / she spent her remaining energy to free herself, did I get that right?
Might be able to help with that one.
That wasn't a Darkside but Xehanort's Guardian and it was really a projection of Ventus (he subconsciously reached out to Aqua), but due to this being during KH 1 his heart is still injured and thus he can't react much less speak.
It wasn't until DDD that Ventus' heart showed signs of being sufficiently healed and stirring.
As for the Guardian "dropping" Aqua and Ven, I'd wager this has to do with Terra going all batshit "This is enough!" and constricting Xehanort with the chains of light as seen before Aqua loses consciousness.
Like Audo and others pointed out already though, it is as if there is a scene missing between this one and the next where Mickey finds her.
It's like watching part 1 and 3 of an episode but missing part 2.