Whenever I play the C right above the staff, it acts as if I`m not putting on the half hole. In order to keep it`s tone I must hold the high C key down which makes it sound airy. Also my D is playing practically an Eb or E. Is there something wrong with my bassoon or is it just an issue of reeds? What can I do to help my crazy C`s and D`s.

well, for the C you`re not supposed to use the half hole lol. You can flick if you want to, but don`t hold the key down! For the D, you are probably pinching the reed. Don`t squeeze the reed! That makes it sharp. Just open up on it. Good luck