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The most common way this happens is when you have a repeating action. Checking off an action creates the next repetition of the action. So if you check off the same action on 2 different devices, each one will create a copy of the action, and you'll end up with 2 copies of the action. The way to avoid that is to not mark an action complete if you know you've already marked it on another device.

If repeating actions aren't involved in your case, then there might be something more nefarious going on. It may be easier to diagnose if you email our Support Ninjas: omnifocus@omnigroup.com