When using vessel mover to move a ship I had, I then spawned in an aircraft, but when switching back to the ship, it had gone from it's position in the water, to falling from the sky at an angle, with all 16 PAC-3 missiles loose from the patriot launcher. From the aircraft's perspective, the ship had been in the water during take off, but once I got around 3 km from it, it suddenly popped into the sky. I can provide a modlist if required.
Note: Ship was spawned naturally, not with vessel mover, so no issue with spawn locator not detecting water.
Potato quality video (KSP only runs on one core) https://goo.gl/eZO8zO
Due to crappy videography skills, it has been proven that the problem can be replicated over and over again.