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.
Is this still an issue in the most recent versions (currently that is 1.10.2, or 16w43a) of Minecraft? If so, please update the affected versions and help us keeping this ticket updated from time to time. If you are the owner/reporter of this ticket, you can modify the affected version(s) yourself.