At least, not yet, but driving another character's personal vehicle may have something to do with it.
It's a dilemma any car owner can empathize with: GTA players claim that their garages are devouring their tricked-out vehicles. The bug seems to affect upgraded vehicles in particular, and may kick in after mission completion. One minute the car's there, shining, magnificent; the next, gone, as if it had never been. Rockstar isn't sure how this happens, but wonders if the trigger is driving another character's personal vehicle. It doesn't have a means of getting the car back once it vanishes into the car hole's capricious maw.
Rockstar points out that a vehicle doesn't switch garages overnight, like some four-wheeled Flying Dutchman. If you leave it in Safehouse A's garage, it will stay in Safehouse A's garage; it doesn't also appear in Safehouses B and C as well. That's a design feature, not a bug. Though, if you're really lucky, you might have the experience one Guardian journalist claims to have had, when his garage spawned two cars where only one was before.
Rockstar's working on the problem. "In the meantime," it says, "please try to avoid parking a car in a garage, driving one already in a garage, or getting in a default vehicle, when playing as a character other than the one with your upgrades."