When you select the pathfinder monk archetyp "Hamatulatsu Master" from Inner Sea Combat setting, you lose access to all of your monk bonus feats [You don't get any Monk Bonus feat in the list, like you don't have them in the first place]. I'm no expert in programming at all but the following is my opinion on it:
The archetyp "Hamatulatsu Master" (HM) alters the bonus feat list and it could collide with the standard monk list in some way. In addition the HM can choose to give up bonus feats in favor for additional stunning fist / day. But in the character sheet the number of stunning fist / day ist not altered which looks for me like it does not automatically choose additional stunning fist / day over bonus feat. (At the same time I was not able to find an option to choose additional stunning fist / day over bonus feats).
Windows 10, Module Inner Sea Combat.