the other reason could be that some new fares (dual inventory) can't be accessed over phone nor work with TA and even with ba.com upgrades.
I had a situation where the ticket I was looking at in WTP showed as £515 ish and there was UUA space but whenever I tried to book as 'book and upgrade using avios', it jumped to £1200 ish. I called and that's the only fare the agent could find.
so agent and I agreed that I should just book the £515 fare, then call back and UUA and it worked a treat.