I expect these are warnings that occur during @auto_tlrc. You can safely ignore these. The warnings occur during the 3drefit commands called by that script. The warning is to let the user know that changing the space and not the view might cause problems. The "view" is essentially the AFNI format suffix, +tlrc or +orig usually. The space is the template space of the dataset - MNI, TLRC, TT_N27, D99_macaque, waxholm_rat,.... @auto_tlrc applies the space of the template dataset and a +tlrc view to the output of the script, the data aligned to the template. Both NIFTI and AFNI format datasets have both a space and the equivalent of an AFNI view whenever a dataset is read into memory. You can see the space and AFNI view of all datasets in a directory with this command.
3dinfo -space -av_space -prefix *.HEAD *.nii*
