Clenching with Invisalign. Could doing this affect my treatment in a bad way?

Though clenching is not something to encourage due to the excessive wear it puts on teeth and the problems it can cause with jaw joints, it actually makes the aligners work more effectively by fulling seating the tray which maximizes the corrective pressures used to move teeth.

I would not be concerned. My observation has been that many patients,including me when I had treatment, will clench more than normal.  From my experience the clenching actually will help move the teeth faster.