Currently Sudoku has two methods for warning users of errors.

If there are multiple numbers in a line or box the numbers are both highlighted in red.
If a square is unfillable it is shown with a black X if Tools>Warn about unfillable squares is selected.

Proposal:
Remove the unfillable square setting with "Show Mistakes".
When enabled this shows unfillable squares with a red X and duplicate numbers in red.
When disabled nothing is shown on an error (i.e. how it would be if you used paper to solve the puzzle).

This setting should be on by default.