If a repeating task is checked off on *both* the mac and the iPhone, both will create their own 'next time' copy of the action. After sync, each gets the other's copy, which can be a little confusing.
If that doesn't sound like what you're seeing, please zip up a copy of your OmniFocus database and send it to the
support ninjas with some info on which tasks are the ones that look wrong to you. We'll try and figure out what happened and get it fixed if it's a bug.
That's the only thing similar to what you're describing that I can think of, though...