My guess would be you might have screwed up a glitch either duping or merging without knowing idk, since you claim to have not moved a vehicle to a slot it shouldn't be in.
I have never in my 6 years of playing GTA 5 online ever caused or heard of a dead spot being created by duping or merging...
A car slot can not create another car dead slot. It has to be either BMX, Aircraft, SV, or Cerburus slot in arena.
A dead slot is caused by a vehicle being in the slot that shouldn't be in it. A car is supposed to be in a car slot, so it isn't the cause.
Or you have an invisible car in the slot...
The podium car doesn't work either for dead spots.
I had all my garages full except the 5 dead spots I have and it wouldn't automatically put it in a dead spot it made me choose a car to overwrite. Wouldn't allow me to put it in the "empty" slot caused by dead slot.
2 dead spots are from...