I'm positive it will only continuously shoot because you've held the shoot button. If you let it go you should be able to move more freely. In a regimen it's usually better to knock down the Balloons bots first, and then aim for the weak sections of the main target.
After a certain point (when you've hit enough weak point I'm guessing) there will come a red weak point, which stays for pretty long. Yellow balls are more useful here, as you can then pound that one weak spot several times and getting big damage off.