So, you separated a rover, or built one from scratch, or undocked your craft with the inline docking port, or messed in some other way, that root part is out of whack and your craft defaults to a wonky orientation. You must remember to switch "control from" every time you go to it, or you'll perform a burn in a totally wrong direction, or your wheels turn all wrong.   tl;dr: KAS-attach the part you want to be root to a space station, go to KSC, go back, detach. note, KAS-attach, n