It's possible that you stressed the port pins beyond limits. To protect the port pins against negative or overvoltage, they have clamp diodes connected to VCC and GND. However, if you stress them too much, they may melt and either break (leaving the port pin unprotected) or short (making the port pin permanent GND or VCC).
The bridge circuit should have protected the port pins against inductive transients from the motor, but depending on your exact circuitry, things may have gone wrong.