How to replicate:

• put one Diamond (or whatever item/block you like) into an TE Cache
• place the Cache on the back of Digital Miner
• turn Auto-Eject on
• insert Gravel (or whatever blocks you dislike) into Miners inventory
  --> all your Gravel will be turned into Diamonds :)

used Versions:
Mekanism 8.1.1.219
TE 4.0.0-176

Post your CoFHCore version, remember that CoFHCore-[1.7.10]3.0.2-263 (yes the alpha) changed what can be imported into a cache and what can't be. Try to replicate the issue with that version.

I had that issue with CoFHCore-[1.7.10]3.0.1-254.jar

Now tested with CoFHCore-[1.7.10]3.0.2-269.jar (only 6 hours old) but still the same.
I can duplicate whatever item i want using TE Cache with Digital Miner.

One item type mass storage like a ^ barrel or MFR deep storage unit.

Huh, I'll take a look. I don't think my auto eject implementation could cause that, though...

What exactly is the TE cache used for?

Just realized, the same happens with other machines also if they are set to eject their output directly into TE Cache. (e.g. for mass smelting cobble into smooth stone)
If i try to smelt something else with that setup, the caches item count is still increased regardless if the item type matches.

Edit: TE Cache = Thermal Expansion Cache, one block mass storage which can hold up to 640k of one item type.
I also tested JABBA barrels but this seem to be Ok.

Maybe @KingLemming could shed some light on the issue.

Seems like a TE issue then. Closing until further notice