This has actually bugged me ever since i saw 'The Journey's End' the first time but I only recently bothered thinking about it in-depth.
Back in 'The Journey's End' when The Doctor is shot by a Dalek he regenerates but instead of changing his form he uses the energy to repair his body then directs the excess energy into his hand so he doesn't need to change.
The exact quote he explains it with:
'I used the regeneration energy to heal myself but as soon as that was done, I didn't need to change, I didn't want to, why would I? Look at me. *adjusts tie* So to stop the energy going all the way I siphoned off the rest into a handy biomatching receptical, namely my hand, my hand there, my handy spare hand.'
It was first stated in The Deadly Assassin that a Time Lord can regenerate twelve times before dying (thirteen incarnations in all). - "The Deadly Assassin". Robert Holmes, David Maloney. Season 14. British Broadcasting Corporation. 1976.
Does this mean that the Doctor is infact on his 12th incarnation?