I had a similar problem: The "Thunderbolt display firmware update 1.2" kept reappearing in AppStore, even though the uppdate seemed successful.
According to Apple[1] the update was successful when the the Firmware Version is 26.2 and the Port Micro Firmware Version is 2.0.7 (visible in About this Mac -> SystemReport).
Above versions were correct in my case, but the update still kept appering in AppStore... (probably I did download and install the update manually after the first failure, but I don't remember ...)
To get rid of the annoying update in AppStore I used the softwareupdate command[2] on the commandline:
softwareupdate --ignore TBdisplayFWUpdate1.2
[1]: https://support.apple.com/en-us/HT204450
[2]: https://developer.apple.com/library/mac/documentation/Darwin/Reference/ManPages/ man8/softwareupdate.8.html