She had more cs but more of that was lane cs. Jax farmed jungle monsters, which give more gold per cs because it takes longer to farm them. This cs score tells me that Jax out farmed her later in the game, or she would have been significantly behind in cs due to killing jungle creeps throughout the early game. Her cs advantage should be much higher if she was actually oufarming him.
As for having more kills, that means nothing without context. If Vayne got fed early, she might have gotten 6-8 kills on the enemy bot lane until they were each worth only 100 gold. Meanwhile, Jax cold have been getting shutdowns. His team could have had more barons or towers which would give him more gold. Context is everything here, and we have no context. From what we know, it looks perfectly fair.