If a rotor has one or more side seals stuck in the grooves, does that mean that there is a mechanical problem with the rotor, or that they simply are jammed from carbon and other buildup? I just want to make sure before I buy some rotors for my rebuild. TIA.

Usually, its just carbon and gunk built up in it becuase of it sitting for a long time.

as long as they arent rusted in you're prolly ok

I had a stuck side seal in one of my rotors and it was from the face of the rotor getting dented some how cause a pinch in the side seals area.