I am missing a couple of teeth as they just never formed and a wisdom tooth filled that gap its been there for 3 months no issues is it okay to leave it in there permanently?

If the teeth that never formed are 2nd molars (which is extremely rare) and the wisdom tooth erupted into that space, there should be no further issues. Have your dentist take a look at your next examination.

How do you know that you are missing teeth that never formed You need x-rays to confirm this, now see your dentist for an exam. If space is closed than your bite should be normal.

Please see or Dentist for a clinical examination and appropriate x-rays. This bill enable your Dentist evaluate your occlusion (your bite), the positions of your teeth, the presence or absence of specific teeth, the angulation of the roots of the new erupted teeth, and the health of the supporting bone & gum tissues. Impossible to answer your question without physical evaluation. See your Dentist.