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One possibility here is that the calendar export feature is being used.

OmniFocus updates that calendar file every time you sync, but that doesn't necessarily mean that Calendar on the phone will notice that the exported calendar file has been updated before the appointed time.

If that's the case, it may help to use "Mail, Contacts, Calendars" to change the "Fetch New Data" setting on your device. If the phone checks those accounts more frequently, you've got a better chance of heading those alerts off.

It won't completely eliminate the chance of that happening, though. We can lead their app to data but we can't make it sync, if I may mangle an old folk saying. ;-)

If you don't have the calendar export enabled, contact our support ninjas and we can investigate this with you. If you're only using local notifications, you should be seeing the behavior you're requesting - checking an action off cancels the reminder.