Bite off with Only 5 Weeks of Invisalign Treatment Left

I have 5 weeks (of a 20 week period) left on my Invisilign to correct two slightly protruding teeth (one upper, one lower). However, when I remove my trays, my bite is off so much that it causes a dull ache in both sides of my lower jaw. My orthodontist tells me it may be something I have to learn to live with. I did not have the problem before the Invisilign. Is this something that can be corrected with additional trays after the final impressions for my retainer are made?