Hello,
We know about such types of PEVerify errors, we believe it should be marked as warnings in PEVerify, not error, because PEVerify execution does not return error code (PEVerify exit code equals 0, it means that assembly is valid, in other cases status icon in ILProtector will be red), but PEVerify displays these situations as errors. Next, about reason why it appears. PEVerify can't resolve referenced assemblies and types and displays errors. It can occurs when protected assemblies are copied into different folder without referenced assemblies. Copy referenced assemblies too and PEVerify error should be disappeared.
In simple words, there are no protection errors (if you see green status after protection).
Regards,
VgrSoft