Hoppers now appear to push items downwards simultanious to when they suck them up from above.
That means that in a vertical hopper tower, there will be 2 items at a time moving downwards.
This won't happen if the top hopper isn't facing down onto the other hopper underneath.
Steps to reproduce:
1. build a hopper tower of at least 3 hoppers
2. put a stack of items in the one on the top
3. observe the behavior of the hoppers
Gfycat of the process
Isn't it like that in 1.9.4 and earlier versions as well?
edit: Does MC-102994 describe your issue?