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Are you sure you didn't uncheck it instead of using Undo? In my experience, Undo does the right thing with completed actions (repeating or not) in 1.9.

Alternatively, are you using OmniFocus on more than one device, and syncing? You can get duplicates of repeating actions if you mark the action complete on two or more devices.

If neither of those apply, the next time you get a duplicate action, immediately contact the Omni support staff, and they can do an analysis of the transaction history in your database.