I use Gorilla Glue (polyurethane) for pens. I always leave them overnight to cure. Here are a few tricks that work for me:
* I use an engineer's depth gauge to measure the tube inside the blank, then mark that depth on the outside of the blank. After that, I trim the blank on the bandsaw, just outside the line. I may use the bandsaw to trim tiny "bites", almost like using the tooth "set" on the blade to "sand off" a tiny bit of the blank to bring it closer to the tube before milling. It is easy, and limits wear on the pen mill.
* On the other side of the blank, where the tube was glued close to the end of the blank, I use a 1/2 inch chisel to scrape off the excess glue on the outside of the blank. Be careful not to cut yourself with the chisel. It helps to clamp the pen blank in a handscrew clamp or a vise. My reasoning for trimming with a chisel is simple: it is easier for me to sharpen chisels than pen mills. Why dull the pen mill on the hardened glue? The real wood is softer.
* I manually insert and twirl the pen mill "drill" into the tube at both ends to knock out any glue "plugs". I manually clean out the tube(s). I tried Play-Doh plugs, but it was messier to clean up Play-Doh than the dried polyurethane glue. I bought some dental wax to try, but keep forgetting to try it.
* If any glue remains in the tube, try cleaning it out by gently twirling a round file inside the tube. It is very rare that I need to do this. (I agree with the others; I think that your mill may be stuck when some of this residual glue melted from friction, then hardened.)
* Next, I square the ends using the pen mill on a small benchtop drill press. I use a handscrew clamp with one screw against the drill press post to keep it from rotating. I insert the blank in the drill, support it with a waste piece underneath, test the up/down motion of the drill press in the blank to make sure it is loose and moves freely before turning on the drill press, and then mill the blank. I am gentle with the drill press, stopping it often to inspect the blank. Stop if you see shiny brass!
* Turn off the drill press, slide the waste piece out, slide the blank off the drill/mill, repeat for the next blank.