I solved the problem. He mentions it in passing in the tutorial, but it’s very important to use a sequence of images as opposed to a movie clip. Everything is aligned now.
I am following a tutorial here: https://www.youtube.com/watch?v=kfGXRsaBf5U After I finished tracking the dots on my fingers (right and left hand) and in the 3d Viewport selected Reconstruction > Link Empty to Track, I noticed the empty is not following the dots exactly. Can someone tell me what I am doing wrong?