FPGA's will help you develop your "theoretical" digital skills much faster, but your practical skills will suffer. If the course is well designed, the time gained by not using breadboards should be dedicated to practical problems.
People here have already mentioned quite a lot of them (groundbounce, race conditions, etc.). Though you might never encounter these anymore (e.g. your synthesizer takes care of race conditions, setup-and-hold, ...), you need to know that things differ from theory to practice. Else, you end up with engineers who design circuits, the circuit gets up prototyped, and eventually never works. This is because some issue has popped up, which went undiscovered in the design phase because one didn't study the design critically enough.
You could put 1000 monkeys writing HDL/spice, and at least one will write the circuits you want. But that doesn't make him an engineer.