toilet is continually clogged
If the wax seal is misaligned enough it could potentially lead to clogging, though I would also expect water on the floor if that is the case.

If the toilet was just seated poorly, then your risks are escape of gas and escape of sewage. 

Frequent clogs are usually caused by an obstruction, either in the toilet itself or downstream.  Venting problems usually manifest as gurgling or slow draining versus a complete clog.