I generally use a CA finish on all my wood pens, and I've never had this issue crop up on me. This may be due to the process I use to prep the pen blank right before applying the finish.
First, I turn the blank to my desired profile and sand it to finished profile with 220 grit dry. Next, I bump it up to 500 grit dry, followed by a wipe with RUBBING ALCOHOL, which will dry pretty fast. Then I go back over it with 500 grit as the blank is drying. After that, I do the same again with 1000 grit. Wipe with isopropyl, run over it again with 1000 grit. By now, the wood surface looks nice and uniformly shiny and is very dry.
At this time, I make a single application of Minwax Stain and Seal (color - natural). This wets the wood appearance really well, and ends up reacting with the CA that is applied right after while it's still wet. The CA ends up bonding to the Minwax and wood instantly. I use a pretty heavy first coat. I immediately (it's already dry) apply a second heavy coat of CA from the OPPOSITE direction. I only spend seconds with my blue shop paper towels in contact with the pen barrels (any more and I risk getting little blue paper bits stuck to my work).
I then wait a good 5 minutes between coats of CA, going from one side, then the other, till I have 6 to 9 coats on the pen. The CA that I use is just the 10-packs of disposable tubes made by Harbor Freight Tools for $2.99... It's medium thickness stuff, I think, though it also runs pretty quick when I'm glueing up my blanks.
As for final sanding and polish, I start at 1000 grit (all sanding from here on is wet) to knock down any surface ridging and flatten it all, and turn the lathe off after to sand "with the grain" to remove any surface ridging that the sandpaper may have caused. I do this "with the grain" sanding every time I jump a number of grits or every other grit.
After 1000 grit, jump to 3200/3400, then 4000, 6000, 8000, 12,000. After the 12k, I use Meguiar's PlastX (which works just like One-Step Plastic Polish, only cheaper), and finish up with Turtle Wax Hard Coat.
It's a long process, but the results look spectacular.