According to the Rambam, the gemarah in Sanhedrin is about Yoshka.
By context and content that gemarah seems to be suggesting that it was the Sanhedrin who killed him. It also says that he got skilah and only had 5 students as opposed to 12 that the goyim say.
When you consider that the goyishe books were only first written half a century after they believe Yoshke died – and that the person describing his life NEVER EVEN MET HIM, (never mind the fact that each of their books have contradicting stories for just about every major occurrence in their descriptions of his life) its no wonder why there is such a divergence between what the gemarah says and what, lehavdil, the goyim say.