Sometimes duplicate cells are intentional; if you want to override DRV's defaults, you can add this line to your .calibrewb_workspace/readerprefs file to make it a warning instead of an error:
exceptionSeverity DUPLICATE_CELL 4
(Usually if your workflow knowingly creates duplicates, the people who write the Calibre rule file have added a Layout Input Exception Severity setting already; "This is Not Sam" is probably correct about the GDS shouldn't have it in the first place.)
Best-
Sam.