Might be something that the 1.0 update broke.

EDIT: Lutin said he experienced this bug on 0.90.

For me it always selects a packrat I crashed on Mun when this happens.

Also nice to note, if I recover the vehicle instead that is controlled, I lose the ability to click and interact with KSC buildings

This one is really annoying, but I'm unsure if we can fix it from our side. I believe KSP is indexing by a number, and if vessels are removed before pressing fly it shifts and you'll end up looking at another vessel :-/

@godarklight maybe check if the selected vessel is the one we're looking for, and not an asteroid?

I'll look to see if I can find the log for when it happened.