Is invisalign cause of my headaches?

It maybe wise to see your Invisalign dentist to report this.

A possible theory is that being a new object in the mouth (the aligners), your brain (whilst you are sleeping) is trying to fit the upper and lower teeth together as much as possible and the aligners are in the way. So the brain is getting your muscles to move your jaw around to get the upper and lower teeth to sit as they once were (before the aligners). By doing this so much whilst your as sleep the muscles get tired, full of lactic acid (as if you have done exercise) and are very tense; similiar to cramp. This could be manifested as a headache.

A thorough examination done by the dentist could identify the muscles responsible and try to identify a solution for you.