Yes, a vacuum-formed retainer should cover all your teeth. And here’s an online post describing what can happen if it doesn’t:
“I have noticed that only my back molar teeth are touching and none of the other teeth in my mouth actually meet. This has occurred after about one year of wearing what I believe is a vacuum formed retainer that does not cover my back molars. I completed the Invisalign treatment about a year ago and my teeth looked perfect after. I am wondering why my orthodontist would give me a retainer that didn’t cover all my teeth?”
There is a major risk wearing a vacuum formed retainer that does not cover the biting surfaces of all of your teeth. The most significant risk is having the teeth hyper erupt which is exactly what sounds like happened to yours. If this is happening to you, you should immediately return to the doctor who treated your case and express your concerns.