It sounds like your images are not plate-solved (i.e. don't have WCS coordinates in the fits headers). If that is the case, you can disable the "Use RA/Dec to locate aperture positions" option in the Multi-Aperture set-up panel.
If you'd prefer to plate solve first, either outside AIJ or or using AIJ's astrometry feature (
), then the RA/Dec option should work.
If only a subset of images are plate-solved, the turn off "Halt processing on WCS or centroid error", and as long as the first image is plate solved, the photometry should proceed with Use RA/Dec enabled. This mode can be handy if you have a meridian flip or large jump in tracking. Then only the first image and any image after a large change in the position of the filed on the detector need to be plate-solved.
Karen