I don't know if this is a DATA or CODE issue. Simple way to see this problem:
Create a new Human PC, 10’s for all stats.
Add 1 level of rogue. You now have 9 skill points at 1st level, all of which have to be assigned to different skills so you have to 1 rank in each of 9 skills. Assign them. You now have 9 trained skills with 1 rank each.
Add a level in fighter. You get 3 more skill points to assign.
You now have 12 skill points total and 9 have already been assigned with 3 left.
Assign the 3 remaining points to 3 of the skills that already have 1 skill point in, aking them 2 ranks each.
Now remove 1 skill point from 3 of the remaining skills that still have 1 rank and assign them to the other 3 skills that have 1 rank. You should now have only 6 trained skills with 2 ranks each.
PCGen doesn't allow you do the last step which is completely legal since skill ponts can be retrained under Ultimate Campaign. You can remove a skill point previously assigned in an earlier level and apply it to any other skill, even if that would make the the earlier level's selection invalid. The legality of any skill point distribution is judged solely on the current level of the character. In the case above the current version of the character is 2 levels and 12 total skill points. So those 12 points can be distributed as 2 points for each of 6 skills.
For reference: It's not just for retraining. Paizo published characters before UC retraining have skills assigned without regard to whether they would be possible at a previous character levels. The evidence from Paizo examples is that it's clearly the intent that NPCs not be bound by this per-level legal allocation requirement; although it is could be inferred for PCs according to Core Rules page 30 section on "Advancing Your Character". However, as a consequence of UC defining how retraining works, it's pretty clear to me that even regular PCs probably didn't explicitly have that restriction either.