Aligners are made of a hard, clear material about 1 mm thick and cover the teeth on all sides. This means that when your aligners are in, you're biting together not on your teeth but on the aligners. It feels as if something high has been placed on your teeth. This awkward feeling gradually fades during treatment, and after about 3 months your teeth feel less comfortable without the aligners than with them. The reason is that the teeth shift and adapt to the aligners, making room for them in the mouth. So when we take them out, at some point it feels as if something is missing. This is a temporary change in the position of the back teeth, caused by wearing aligners for a long time. After treatment ends, the contacts between the back teeth are gradually restored.
This answer is for general information. Your own case needs an examination by an orthodontist.