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. Unfortunately, we do not currently have a workaround to recover a car if it is missing. If you would like to receive an automatic email notification as soon as there is more information, please log into the Support Site and click Subscribe at the top of this page. Also please note that vehicles saves in the garage of one safehouse (Franklin’s Aunt’s) may not show up in the garage of a different safehouse (Franklin’s Vinewood Hills).
This issue may occur if you drive another character’s personal vehicle. We are looking into a fix to prevent this from occurring in the future. If you would like to receive an automatic email notification when the fix is live, please log into the Support Site and click Subscribe at the top of this page. 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.
So while there is no workaround for this glitch, please keep your eyes peeled on the Support Forums and also subscribe to be notified of a fix.
Source: RockStarGames Support