Sorry for the double post, but I believe I have worked out the issue.
The speciality system on SL uses a caching system, which means it saves the something when it first loads it, so instead of reloading that data each time, it just brings up the saved file, to reduce strain on the server.
But sometimes the system doesn't notice some changes, some might have seen this in the KG's, but checks have been put in place to overcome it.
However, in this case there are no checks, so the system still thinks you have x chakra points, and it does check when you use the jutsu.
The problem would easily be solved, by just adding a check to the specialities, to check that the user does have x chakra points, and if they don't, stops the jutsu being activated, and updates the display.