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

It is not unusual to have trays not seat as planned, and often some fine tuning is needed.  This is less convenient with Invisalign, since new impressions are needed (this is called "mid course correction).  These are sent back to Invisalign for a new set of trays. 

 

This isn't "starting over" since a lot of progress has already happened, but the aligners that have been made will no longer work.

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.