The irony of losing a fancy car you've spent thousands of dollars customizing is thick in GTA 5, wherein the chances are good you deprived some other rich jerk of that car in the first place. That doesn't make a bug which vanishes stored vehicles from garages after completing missions any less of a bummer, though.
Rockstar has created a support page about the bug which offers a bit of insight into the problem:
"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," the page states. "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."
Rockstar does not have any means of recovering cars that have disappeared into Blue Hell, so take care with any vehicles you've become attached to.