Yes, that message can be ignored. AIJ has moved to using a different library for reading in FITS images, and it is more strict about what it excepts. So if the file has any violations for the format (
you can test here), then it fails. "Legacy reader" is just imagej's custom reader.
AIJ shouldn't be outputting something invalid, so I will look into that. Would it be possible for you to provide a copy of the image?