I've seen this happen enough times myself, most notably on Sharqi. I'll see the flag capture bar immediately once I spawn even though I am not within the capture radius. Typically this occurs when I spawn at a non-capturable base.
When this happens, I am able to move the flag up and down, but unable to actually convert control of any point. (Thus if you have this show up, don't try capping flags, because you'll actually not just not cap it yourself, but also prevent your teammates from doing it while you are there)
Solutions I have found to avoid this problem when I see the flag capture meter while not by a flag:
1. Get into a vehicle and then exit the vehicle.
2. Go to another friendly flag, get inside the capture zone, and exit the capture zone.
IMO, the vehicle trick is usually far faster to remove the false capturing status that causes this glitch.
Hope this helps.