Hopper-Clock duplicates items on world restart

A simple hopper clock, located close to [0,0,0], containing only 1 item to create an alternating signal for a warp hub, clogs up after a while, since the contained item duplicates (e.g. diamonds). Duplication is not caused by teleporting away.
Spawnpoint is at [32,73,256], seed = "0", average warp distance is 2km, since all players are there most of the times. Duplication might be caused by Server restart, (since it's auto-restarted by the host).
This contraption could be build in Survival.
The exact locations of the hoppers are [2,7,1] and [2,7,2]