It's at 99% (since if I punch or do a small ki blast it will be 100 and then the blue gauge disappeares) but I still got the point

Sorry, I don't understand your problem. Please read the FAQ: how to post a proper bug report. Thanks.

The special attack's blue gauge is supposed to disappear when we recieve a point. which is when we reach 100%. But when the gauge is filled to 99% (since the blue gauge is still there), we still recieve a point

it works exactly as intended: 100% = full

One full bar = 1 SP
So that you know that your SP BAR is full.

Clear example: if you reach your SP MAX (5) then the bar is full instead of being empty.