I'm creating a human Druid 9, with Nature Bond Domain: Weather.
When I select it, initially it's OK, but after a while I get an error
"Too many Domain Alternative ~ Inquisition have been selected - some need to be removed"
The link takes me to Class Features where I find I have -1 of these... not 0, not +1 but -1.
pathfinder core rule set
Now I know I'm tired... derp.
Druid wasn't setting any ClericDomain value, defaulted to 0, you took -1 for being granted a Domain by the Druid, ergo the -1.
Okay, got this figured out now.
I started by removing all steps of the Domain from the submitted character, saving, re-opening (no error), added Domain, choices & spells, saved & re-opened. Same error.
cleared everything out, new character, most options not bothered with, just Human, add Wisdom, set alignment, add Druid 5.
Select Nature Bond = Domain, Class Feature > Domain = Weather,
Domains, select Weather
Spells Prepared, select the 3 domain spells.
Save, re-open - same error.
shorter version: just new character, add Wis, Human, Align=Neutral, add Druid 5.
Class Features: Nature Bond = Domain, Druid Domain = Weather, (no error) save, re-open.... (error about Inquisitions)
Oddly - if I compare the file saved from creating him, thern that from re-open and re-save, the only difference is default skills are added 2nd time round. There's nothing in the PCG that mentions Alternative, Inquisition or any obvious relation...
You won't either. It's hidden in "Domains".
Tested, works for me now.