There's been some questions posted on the Rockstar support page relating to vehicles and their upgrades - it seems they're growing legs and walking off.
An example of one of the questions is: "I've lost some of my upgrades after completing some missions and then checking my garage. What should I do?"
Rockstar's response, you ask?
"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 may not show up in the garage of a different safehouse."
In short: Stop moaning and wait, we'll fix it eventually.Rockstar have already given us some advice on general bug fixes - check those here.