I sadly am unable to repeat this bug after rebooting the game, so I'm posting this comedy rather then as a bug report.
Although this bug is incredibly entertaining, it is a bug.
It most likely has something to do with clipping the armed landing gear with other parts. This craft spawns under the launchpad and performs the landing gear bounce down there, rather than the usual spawning on top of the runway and bouncing. I thought it was just the runway at the start but upon further investigation it appears as though this craft clips completely through every single structure in the KSC with exception of the actual ground. Kerbal can still enter and exit the craft, although the kerbal is also nocliped on everything.