I've been racking my brain on this one, here's what I have. I have UBNT clients connecting to UBNT AP's connected to MT Switches and at certain sites those switches connected to Cisco routers (for the time being, they will be swapped out with CCR by end of the year). Now UBNT has this weird glitch that seems to happen with Thunderstorms or power spikes, when this occurs a unit will freak out, drop its LAN connection and on my Cisco router I will see a duplicate IP address error for the IPs on that local interface, if not caught right away it will take down that interface. Now I don't expect a solution for UBNT but I'm wondering if there's a way I can block this on my MT Switches. Maybe block those IP's from coming back from the Client, through the AP to the Switch. I really don't know if anyone might be able to guide me on this, like a firewall rule that would be greatly appreciated.

Your story is a bit misty on how happens what and when...
But to make some rule to block some IP (the double one) you have to know which one is original and which one is double? You can only find out by the mac address.... so you have to work with mac address.

I think first you need to investigate what really happens and tell us so we can give some advice....

So what happens to the ubnt client is basically either static electricity build up or a power spike blowing out the LAN port on the radio. Sometimes that's all that happens and we have to replace the radio, but other times it will kind of create a loopback almost where the radio will create a duplicate IP address of the local interface on that sites router.
For example:
%IP-4-DUPADDR: Duplicate address 10.0.1.1 on GigabitEthernet10/0/0, sourced by 0027.225e.a94d

That MAC address being the MAC address of the UBNT device. Now ubnt has said well its a grounding issue, you needed shielded cable, shielded ends and supposedly the latest firmware update resolved it. Well it didn't, we do all our installs with shielded cable, shielded ends and we have our techs verify with a cable tester that shows its shielded all the way through. So since I've yet to find an actual solution I'm trying to find a way to prevent it from affecting an entire tower site by somehow not allowing that duplicate IP address to come back through to the router.