My game uses a similar system, this can be solved with a bunch of duplicates done to your moves (or possibly simpler methods.)
To explain, let me give an example with Scorpion's spear: Say you have the move named "Spear", you execute the move and he uses the spear. If you execute it again, he will do it again, and again, which is what you DON'T want.

To solve this, you would make a clone of the first move (Copy/Paste the move file if on Windows), name it something like "Spear2", or "SpearEnd", and in the Chain Settings of "Spear2", add a Required Move slot, insert "Spear" in there, and in "Spear", go to the Chain Settings and under the links add "Spear2" in there. Make sure both moves are added to the character. Modify "Spear2"'s properties and animation to whatever you want (in this case a pull in and a punch), and the end result will be Scorpion pulling the opponent with the spear, then when inputted again he will pull them in and punch them.

Hi

I guess you could wait for the next installement of ufe wich will have special gauges per character, and that way you can add some limits to the moves... the other is like Twrmois says, make duplicated versions of your moves so not all of them can chain together again.

in my particular case to stop spaming from the CPU i use the super move gauge to limit certain moves, like hadouken and so, also, you could add more time to your moves recovery animation.