The Radio Times is reporting that Steven Moffat had quite a lot of trouble with the budget for the 50th Anniversary special. Here's the quote: “It was unbelievably tough actually making the 50th...It was extraordinarily difficult mainly because we were trying to push the boat out and as ever we didn’t have enough money. We were making a feature-length Doctor Who on the schedule and budget for an hour. We’re doing it in 3D on the budget for 2D.”
This sort of using-Doctor-Who-as-a-testbed for shiny new special effects isn't unprecedented; as mentioned in "The Writer's Tale", RTD recorded similar woes about the budget for "Planet of the Dead" and "The Waters of Mars". He'd been asked to start making high-def telly but didn't get commensurate funding for it (reading between the lines, it would appear that they pulled it off by cutting some FX shots and the miracles Julie Gardner could work negotiating with other BBC departments to obtain extra funds; unfortunately, Moffat doesn't have a Julie Gardner). We've mentioned the show's funding issues before (and, for that matter, that the BBC has decided to scrap future 3D productions on grounds of not being worth the trouble for money), but Moffat has been fairly discreet about the show's budget up to now. Perhaps that's something to do with why Moffat was so cagey on the length of the anniversary episode, if he wasn't sure how much money he was going to have to work with (and BBC Worldwide, which is putting up part of the funds, just did their annual budget).