By your logic, the 1:01 Joe D 'ran' in the Sat qualifier would have stood even though he went through T3 into T10. Instead, HE went and told them it was wrong. See how it's supposed to work?
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The difference between the two is that in this case T&S was alerted to the error BEFORE the final Q sheet was posted and, hence, it could be fixed.

For the Sunday race, it looks like the problem with the results was not noticed until AFTER the final results were posted. Final is final.

This is another case of there being a communications error, as the flaggers tell control that someone took the shortcut and then the stewards are supposed to call T&S to let them know. I suspect the first happened, but don't know where the error was introduced.