Ran into this recently, tracked it down this morning. Have run a few tests to confirm it isn’t a single task.
I have been using my watch to quickly view tasks when on the road or walking, but haven’t been in the habit of checking off tasks on the watch. This week I checked off a flagged task in my “execution” custom “today” perspective on the watch. In reviewing my tasks today I see that the item wasn’t marked as done on my mac, iphone, and ipad. I opened omnifocus and let it fully sync on all devices and unchecked and rechecked the task done on my watch. Nothing. Everything sync’s fine to my watch, but this checked item doesn’t sync to the phone and onward.
I tried a “due” and another “flagged” in the execution group and it changed the counts on the front page of the watch app, but didn’t sync the checkmarks to my other devices. I then tried a task not in the execution group and it didn’t sync either.
I don’t know how long to wait, so some of my later testing might be faster than the sync window on the watch; not sure. I re-paired the watch and phone, and that didn’t fix it. I looked for sync settings but didn’t see anything.