I have come across a few issues of archetypes that should be compatible, but are not behaving as such.
the first set is Crossblooded and razmiran priest for the sorcerer. Both archetypes should be compatible and work together. However i think i know the issue. The Cross blooded lets you choose which bloodlines bonus spells you recieve. The razmiran Priest replaces 2 of your bloodline spells. Since the crossblooded archetype still leaves you with what functions as bloodline spells, the razmiran priest can still replace them.
There was an errata covering this.
"Archetype: If an archetype replaces a class ability with a more specific version of that ability (or one that works similarly to the replaced ability), does the archetype's ability count as the original ability for the purpose of rules that improve the original ability?
It depends on how the archetype's ability is worded. If the archetype ability says it works like the standard ability, it counts as that ability. If the archetype's ability requires you to make a specific choice for the standard ability, it counts as that ability. Otherwise, the archetype ability doesn't count as the standard ability.
Pathfinder Design Team, 07/12/13"
The quote isn't specifically speaking about a changed feature being replaced, but it does give a clear definition of what changing the feature means and that changing it doesn't necessary mean it isn't the "same class feature." If it is still the same class feature it can then be replaced.
I believe this is also the issue with the scarred witch doctor and winter witch.
the winter witch limits the familiars accesible to the witch, but she still has the familiar class feature. the scarred witch doctor replaces the familiar with its fetish mask, which should still be allowed.
There are likely other examples of this. I may also be reading the faq completely wrong, and everything is working as intended.
Windows 10. i7 processor. 8gb Ram.