Well, I guess now I have to explain the bug I mentioned somewhere else.
Basically, when I timewarp way to god damn fast really quick, sometimes the rocket (because VanillaUpgrades stops the rocket once it enters a SOI) just gets... Well. It gets trapped in this weird place where it can't move. If one tries to navigate to it, delta-v markings and the transfer window won't show up. Engines, fairings, separators, and any other activatable objects do no not function. The delta-v calculator says the delta-v is zero.
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For example, this unfortunate mission to Mercury that ended up in this precarious situation. It is completely stuck, and cannot move.