Generally the only alignment on a bike is trueing wheels. But I can't see how an out of true wheel would lead to a wobble like you describe.

I had a 'Trail-a-bike' when my boy was very young and small. I'm a pretty experienced rider and while I never had a 'wobbling' problem I could feel him throwing his weight around back there sometimes.

If you could find someone with a little bike knowledge to actually watch you and your daughter ride maybe they could spot the problem.

Or try a solo ride and pay a bit of attention to your track as you ride along by observing how well you can maintain a constant distance from the edge of the road or path you're on. I've seen riders that can't seem to ride in an area less than 2 feet wide.