Log those defects

I have seen this again and again, and even been guilty of it myself a time or two... dont debate a defect just log it.

If you are running test scripts and the script doesnt match the system then fail it. This can be revisited to decide if the script or system is in error and corrected. Raise defects for all these errors encountered. This will mean that no one can later come back to you and say "This test will fail it is written wrong, so why have you passed it"

The vital thing is just logging all the defects and failing all the scripts to ensure that nothing is missed.