If a few pictures are misaligned

If one image is significantly misaligned, yet you expect the $(x,y)$ shift of that image to be quite similar to the shift of the image before and/or after, you can edit the `.aln' file by hand and set the pixel shift of that particular image to be the same as the image that comes before and/or after. You can then run the automatic alignment again but with a small value (like 5?) for the pixel shift limit.