Those messages are nothing to worry about. They simply reflect that the energy function landscape didn’t act like the minimizer expected it to. There’s some internal coding reasons this might be the case occasionally, but that’s more for the developers to worry about, rather than people using Rosetta.
This really shouldn’t be an “Error”, and I just committed a fix to remove the “Error” annotation from the info-level message for future release. — Please just ignore them in the mean time.