There have been some issues similar to this in the past, but they have all been resolved, and were not reopened after my comment. The mobs and minecarts are moving slowly in just certain parts of one of my worlds (I'm in 1.9.4 right now).

For example, in this world:
https://dl.dropboxusercontent.com/u/77400058/Eternal%20Survival%20-%20Copy.zip

The minecart at -77, 62, 143 moves really slowly, along with any mobs that are there (it is not FPS lag; the player moves at a normal speed). However, moving a little away from that area, this is not the case, such as with the minecart at 26, 64, 17.