This could turn into a real news item if Rockstar doesn't fix it quickly.
From what I can tell, Rockstar is currently learning that GTA V is messed up in a very major way. It's a franchise that centers itself around cars, but buying and upgrading them is like flushing money down the toilet...
http://support.rockstargames.com/hc/en-us/articles/200218557-Vehicles-disappearing-from-the-GTA-V-garage-or-losing-upgrades
Vehicles disappearing from the GTA V garage, or losing upgrades
Question: I upgraded my car and then completed a mission, and now my car is gone. Help!
Question: I've lost some of my upgrades after completing some missions and then checking my garage. What should I do?
Answer: 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.
Until they fix this, there's no reason to buy cars, upgrade cars, or buy garages. What a major setback from an otherwise outstanding game. It knocks my opinion of the game from an A to about a B-.