Upset stomach. Is it caused by invisalign?

Possibly if you are not chewing your food as well during treatment.  I would suggest smaller bits and thorough chewing and avoid swallowing larg bites.

This is coincidental. Pressure on teeth is not related to gastrointestinal issues. Cosider seeing your physician. 

Are you sure you are not having any regurgitations or any allergy to plastics. Invisalign can not give stomach upsets. See your GP and I would suggest, stop treatment until you get this sorted. Invisalign needs 22 hours wear time per day. If you are not going to be able to do that, its not going to give results.