On my machine, if the foot is just a little too high off the quilt top it sometimes skips a stitch or two.

There are a lot of different things that can make skipped stitches, as the various answers state. If we knew what longarm machine you quilt with, we might be able to pinpoint the problem.

Because you say there is a needle hole and the skip is due to the needle not picking up the bobbin thread, I would rule out the encoders immediately. I would suspect your needle bar height isn't quite right or the needle is not in correctly. You probably are not out of timing because it would be happening a lot more than "occasionally" if it was timing. Do you notice it a lot more going in any particular direction like when moving the machine away from you or right to left?