This has nothing to do with Bulgakov, but I know there's been a scientific argument about whether it was actually possible for someone to be held at a cross with the nails through his palms. I believe the conclusion was that the body weight would reap the palms and the only way to do this using nails was to drive them through the wrists, which contradics most if not all of the depictions of the event.

Back to Bulgakov. I don't think he was trying to tell the Bible story precisely as in the Bilble itself. Why I don't know, but there is a couple of things worth mentioning:
The story is actually told from Master, so it's Master's book we are discussing, not Bulgakov's own. Of course it is written by Bulgakov, but I trust you understand what I mean.
In Russian tradition Jesus is always referred as Иисус, Jerusalem is Иерусалим. In the book they are Иешуа and Ершалаим...

Also, take a look at this link (about paradoxes in Master and Margarita):
http://menippea.narod.ru/