As far as I know it shouldn't, but there's always the chance of something weird going on.
The negative terminal in most vehicles is connected to the body so that fewer cables are required (one run from the positive to a device, then the device is connected to the body to complete the circuit instead of running a negative wire back to the battery).
There are some positive chassis vehicles, where the majority of the wires are negative and the positive is connected to the body. I may be wrong, but I believe no new reverse polarity cars have been built since the 70's.
If there was a short, there may be black marks or there may have been sparks where the battery was touching the body. However, the body is normally painted so it shouldn't be making a circuit.
As a wild guess, there may be an issue with the wiring on / near the battery and when you moved the battery, the short was disconnected. Brittle or cracked wire insulation may be the cause (and hard to spot) or a stray strand sticking out of poorly terminated cables can cause intermittant shorts.
What make and model car do you have?