If the laser is very slightly out of alignment then that can happen. There is a small margin of error that the alignment can have though. A few degrees either way and it'll either stop working altogether or start working normally. Dirt on the disc can make it skip, especially if your laser is going.

If your CPU is under high load, you might have a bottleneck if it can't keep up with I/O read/writes to the drive. You'd probably get longer pauses in that case, rather than short skipping as you would hear on a stereo CD player. The same applies if your CPU is too slow or the load is too high for whatever piece of software you're using.

What software are you using, and what processor have you got?