Misalgined Bite with Invisalign?

I received my first set of aligners for Invisalign Express 5 a week ago. I had terrible discomfort for a few days and by the time the pain finally subdued, I noticed that my bite was a very off when I took them out to eat. I had braces for four years (age 12-16) and I have very little to be corrected besides my request to do some work to fix my overjet. Should my bite, which seemed normal before, be completely off and uncomfortable? I feel like I'm causing more damage than good at this point.