I have a sorting system on my server and since the 1.9 updates some hoppers dont forward items.
This happens to hoppers in a hopper chain that should pass items to the next hopper as well as to hoppers thet should pull out items from the hopper above them.
Therefore items just bulk up somewhere in the system.
Replacing the hoppers seems to fix it temporarily, but after some time the problem appears again and sometimes it starts randomly working again.
I have checked the server log and the server is not overloaded, so tickrate seems not be causing the issue