Invisalign - Spaces Between Bottom of Aligner and Teeth That Aren't Closing? (photo)

The most common reason for an invsalign tray not seating completely is insufficient space between the teeth.  So if originally some trimming of the sides of the teeth was performed or called for, then more needs to be done at this point to allow them to move.  In other words, the aligner is attempting to move the teeth but due to the tight contacts of adjacent teeth, it is not possible.  Have your dentist check these contacts to see about creating more room.

Whenever you have a concern that a tooth is not “tracking” properly or fully into an Invisalign tray and desired movement is not occurring, consult with your orthodontist. The orthodontist can show you a virtual model of your teeth (clincheck) that will show exactly what tooth movements should be occurring with each tray. Sometimes, teeth will actually move out of proper alignment before being brought into an ideal alignment. The approved clincheck will allow you to visual all expected movements.

This is a common observation and usually indicates that tooth movement is occurring more slowly than originally projected. The solution is to take new impressions and plan a new aligner series (mid-course correction or refinement). Check with your orthodontist, but I am quite sure that is what will be recommended.