This is the first time I have encountered this. I selected the "Laser commander" perk at level 22. When I got to level 24 I noticed that "Laser Commander" was available for me to select again. Odd, and In case you're wondering, this is not a ranked perk. Thankfully, I saved just before I leveled up to 24 and reloaded the game because I was curious. I checked my Pip-Boy Stats and noticed that "Laser Commander" was not there. So I leveled up again and re-selected the perk. Afterward, I checked my Stats and noticed I only had 11 perks. At level 24 I should have 12. I recounted multiple times and I've come to the conclusion that my level 22 perk selection did not register. What gives?