Staging or undocking ship parts in orbit in proximity of another player in another vessel misses some updates or the full updates for new vessels. In my case with another player the staging caused an instantaneous intersection and rapid disassembly.

Reference 0:30 - 0:45 in this video:
https://www.youtube.com/watch?v=sprH74IsksA

Fixed a very long time ago :)

EDIT: Except when you're close and you've targetted the vessel, The protovessel load can't spawn in accurately enough and DMP needs to avoid the collision.