Rockstar is actively working to fix a glitch in Grand Theft Auto V that's resulting in some vehicles disappearing from garages or upgrades being lost. The issue occurs on both the Xbox 360 and PS3 versions of the game and mostly involves upgrades, mission states, and another character's personal vehicle.
"We have received some reports about problems with cars and garages, particularly after upgrading and then completing a mission, and are looking into this now," Rockstar stated on their support site (via CVG). "Unfortunately, we do not currently have a workaround to recover a car if it is missing."
This is most likely to occur if one character drives a different character's personal vehicle. Players may also encounter an issue involving vehicles saved in a safehouse garage not appearing in a different safehouse. Rockstar adds, "In the meantime, 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."