Well, I can't see any pits, but then I can't see great.
Generally, if you get a "pit" in your CA finish, it was a bubble. USUALLY this would be caused by attempting to put on too thick a layer. You used thin CA--then I have no idea how you could muster a bubble. Unless the glue is old and more "gel-ly" than thin.
When you saw the condition, before assembling the pen, you could have sanded it down to beneath the "pit". IF you still had a CA coating (did not have to sand to bare wood to get beneath the pit), then you could sand to a shine and call it done. OR, once the pit is removed, build up the CA finish again.
Hope this helps!!