[MC-79154] Hoppers occasionally duplicate items

Server duplicates items in hoppers. After a while, all hopper clocks are getting broken, because there is more than one item in it. I managed to duplicate diamond blocks.

Server Console says:

[13:01:44] [Server thread/WARN]: Fetching addPacket for removed entity
[13:01:44] [Server thread/WARN]: Fetching addPacket for removed entity
[13:01:44] [Server thread/WARN]: Fetching addPacket for removed entity
[13:01:44] [Server thread/WARN]: Fetching addPacket for removed entity
[13:01:44] [Server thread/WARN]: Fetching addPacket for removed entity
[13:01:44] [Server thread/WARN]: Fetching addPacket for removed entity
[13:01:44] [Server thread/WARN]: Fetching addPacket for removed entity
[13:02:23] [Server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 2144ms behind, skipping 42 tick(s)

Edit: I now caught it happening. A hopper speed up so fast, that even a comparator doesn't work anymore. I'm sure this leads to item duplication.

Code analisys by Timothy Miller can be found in this comment.