In RFTools 2.80, the Crafter (Tier 3) regularly crafts extra "nuggets".

In the examples below, the Crafter crafts:

329 Lapis Shards from 36 Lapis (expected 324)
146 Lead Nuggets from 16 Lead (expected 144)
292 Gold Nuggets from 32 Gold (expected 288)
585 Iron Nuggets from 64 Iron (expected 576)

(This is using the Infinity 1.5.1 modpack with Compact Machines added.)

Hmm, perhaps that's why everyone likes my crafter so much :-)
I'll check it out to see where this duping comes from.

Fixed in next release