This should only happen if you are registering FITS files with StarAlignment, and these FITS files have been generated by PixInsight, probably by the ImageCalibration tool, forcing the FITS output format, or by transforming existing XISF files to FITS.
In such case this is not a bug because the FITS format has been deprecated in PixInsight. If you force generation of FITS files from a tool, or transform existing XISF files to the FITS format, and then load them in a tool, then there are no guarantees.
If the above scenaro does not apply, then please provide the files that are causing these issues, so we can analyze them in order to fix a potential problem.