Hello! From my experience, it could be a bug of Gromacs, which should have been resolved with version 2023.
Perhaps the error you encountered is due to some issue with the xtc or tpr file. Please check that both are correct; you might want to try fitting the trajectory and then rerun the command.
Does gmx covar work correctly with the same parameters?
I also encountered a similar issue in GROMACS 2023, but I managed to resolve it by adding the '-3d temp3d.gro' option to the anaeig command. This modification successfully resolved the error.