Why would Invisalign intentionally make my teeth more crooked?

I've finished the original trays, and am now on my second set of refinements. My dentist never took any molds for them, which I found strange. Furthermore, the last tray of each set of refinements were noticeably more crooked than the first tray of each refinement (Tray 6 vs Tray 1 of each). Now my bottom teeth are more crooked than when I finished the original series of trays, but not as crooked as before I started Invisalign. Is there any reason my Invisalign would be prolonged like this?