I haven't been able to 100% reproduce the worst variety of this, but I have observed several occasions. Most dramatically:

[05:03] ok, so check it out. I observed this behavior: I docked to another vessel solo in orbit of Kerbin while another was in orbit of Duna. [The other player was 20 minutes ahead of me. There were no other players on the server at the time.]
[05:03] shortly there after (or immediately, was distracted) my docked vessel got the message "This vessel has changed in the future".
[05:05] then around 30s or so later, my vessel, missing the docked portion, _transported to DUNA_ and started playing back the other player's movements, while still "vessel has been changed in the future". The other player later switched to a vessel around Jool.
[05:05] I then synced to the other player and regained control of the vessel; however, the other players vessel has disappeared
[05:05] they were completely different vessels with different names
[05:07] I also noticed that one of my Long Probe ships, which no one else had launched and they never left LKO - appeared (replacing a vessel?) around Ike

I have been able to reproduce an unending "This vessel has changed in the future". If I create a vessel in SPH that includes a manned pod and a command seat, then I launch my vessel, EVA a kerbal, and board him to the command seat. Upon boarding, KSP will indicate "DOCKED!". At this time, I will often see a "This vessel has changed in the future" message, especially if I reverted to launch or SPH just before launching.

If I'm the futurest subspace, or this is the first time launching, this message may only occur for 10 seconds. If there is another player in a future subspace, then I'll almost always get the message forever, until I sync with that player.

I have noticed during this stuck historic update time that the throttle on my SPH vessel will randomly go up to specific values that I never did, even on previous runs. I presume these are historic replays of inputs from the future player, who is in another ship in another place.