When there is a ghost tnt, and you stand on it for a while [About 5 secs I guess] you will get kicked for "flying".
This is just the flying detection doing its job. Considering the TNT is client-side, the server doesn't detect anything is actually there. What the server does see is someone who is floating in the air a block up for an extended period of time and, thus, kicks them for 'flying'. The only thing I can suggest is to simply avoid standing on the ghost TNT and just break it. Otherwise, I have no clue if we can change the way it detects if someone is flying. We really shouldn't have a problem, though, as I doubt people will generally think standing on TNT in a server called 'TNT Wars' is a good idea.