The Pathfinder source book is Ultimate Wilderness.
A few classes gain free spells that are supposed to be in addition to the number of spells known for any level. For example, one of my current characters is a Hunter, Forester archetype. The Hunter gains a number of spells per level plus the Summon Natures Ally spell whenever they qualify for it. Here is the text from d20PFSRD:
In addition to the spells gained by hunters as they gain levels, each hunter also automatically adds all summon nature’s ally spells to her list of spells known. These spells are added as soon as the hunter is capable of casting them. d20PFSRD Hunter
The Summon Natures Ally spells are added automatically but they are also counting against the total spells known causing me to not be able to select the final spell per spell level, leaving me with one spell less per spell level than I should be able to select.
I have not tested this with other classes that have similar mechanics.
Linux, OpenSuSE Leap 15.0. OpenJDK 11.0.3.
I’m not seeing the proclaimed issue.
As a Hunter 5th level your known is:
6th 0th level, 4 1st level, and 3 2nd levels.
On your “error” screenshot the character clearly has 6, 5, and 4 respectively. The additional +1 for a Free Slot for the Summon Nature’s Ally is already factored in for both 1st and 2nd levels.
OP not familiar with the Hunter Known Progression and miscalculated the anticipated Known.
PCGen correctly adds +1 to the appropriate levels, and even mentions it in the code block to avoid confusion.
###Block: Level progression
The KNOWN are 1 higher than in the book for levels 1+ because all the Summon Nature's Ally spells are automatically known in addition