Hello. I’m using the latest versions of OmniFocus 2 for iPhone, iPad, and Mac.
I don’t use the built-in Flagged perspective much, but it does seem to be off on the iPhone. It’s showing flagged items that are unavailable, which seems odd, but more importantly, on the iPad (and the Mac) the built-in Flagged perspective does NOT show unavailable items.
Here are some screen shots.
iPad - shows 9 flagged items, all are available:
iPhone - shows 20 flagged items, 11 are unavailable: