Also in Vegepygmy you have its 2 claw attacks at -4 they should be +1
I'm afraid Hero Lab currently has trouble with "OR"'s in the weapons listing for a statblock.
What the statblock is listing is the set of equipped weapons and shields that are on the weapon and armor tabs. In this case, having a manufactured weapon (the longspear) equipped makes all natural weapons (the claws) into secondary attacks (-5).
The current workaround for this is to un-equip all of the weapons and shields before generating a statblock - that will come closer to the official statblock format, although I know it's not exactly the same.
This is on my to-do list to solve (or at least handle better), but I'm afraid its not simple, and will take me some time to accomplish - consider the Xill - a race that has 4 arms, each with the option to be used as a natural attack or to hold a manufactured weapon, plus a bite. Or consider a character like Amiri, from the pre-generated characters for adventure path issues 31-36 - she's carrying 6 different weapons around, but the statblock doesn't list 5 of them.