There are certainly some anti synergies that probably shouldn't be. Things that ought to work together but don't.
There are also some anti synergies and are entirely allowable and presumably on purpose, because you are not meant to use both of those things together.
A prime example of the latter, already mentioned in this thread but from the wrong angle, is Crushing Impacts and Boneshatter.
I hate to be the kind of guy outright saying a build choice is wrong, but if you're using both Crushing Impacts and Boneshatter, you're just wrong. Plain and simple.
They aren't just an anti-synergy, they're separate build elements that are not meant to be used together. They should never both be equipped.
Would you pick the Mercenary ascendency that makes all attacks culling, then use Killing Palm?
You use Bone Shatter as your way to heavy stun in a build that doesn't have a better way to do it. You use Crushing Impacts in a build where you want to freely stun without relying on a specific ability. And in that 2nd build, you obviously do not utilize any skill that's meant to be a heaver stun trigger. You made every ability a stun trigger, don't add to the redundancy.