That message comes up during rmsd evaluation. Specifically it comes about during the case where the first two eigenvalues are degenerate when calculating the rotational component of the transform for the rmsd calculation. Instead of basing the calculations off of the first two eigenvectors, it bases it off of the second and third (which aren’t degenerate).
The “is this the right thing” is in reference to the internal code, rather than a reference to anything you’re doing. Unless you’re an rmsd wonk, and are particular about how the numbers are being calculated, you can safely ignore it.