I have attached a world save with the setup that reproduces the problem. It is just a comparator in subtract mode reading from a dropper with a few bits of redstone to finish up the clock and activate the dropper.

It doesn't seem to happen the first time I try after loading the world up, but it always seems to happen within 3 tries of filling the dropper up and having it shoot items out.

Sometimes it only duplicates 3 items, sometimes it nearly doubles the number of items produced.

A quick search for "1.12 dropper dup" did not give any results, so I believe this is the first time this bug is being logged.