if you incapacitate a crossgen figure or wild card version which results in them taking pushing damage. does your figure have to take the click of damage for thier pushing damage. I would rule no because pushing damage is described in the rules as self inflicted even though incapacitate causes this damage. just looking for an answer on this. if you can supply specific faqs on this proving one way or the other would be appreciated.

No for several reasons:
1) Incap deals 0 damage so unless you Enhance/SHIELD the attack or roll a critical hit you don't deal any damage. (Check the PAC)
2) Push damage is not technically "damage" but is instead defined as a click of the dial. (Check the Rulebook and its Glossary)

Pushing damage is something the figure does to himself, so if you Incapacitate a MystiGen figure and they take pushing damage, you will not take any retaliation damage from them.
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So pushing itself is not damage taken, so it will not cause the MystiGen to retaliate. However, if you make a critical hit, Enhance, or add SHIELD damage to your Incapacitate attack, then you WILL cause the MystiGen to retaliate.