Hm, looking into this a bit more, the incompatibility stems from running both Bobs Mining Drills and Extended Vanilla Mining Drills. Running either mod by itself works just fine, and all mini mining drills are properly copied without errors; the error only appears when attempting to run both.
I don't think there's much reason to use both, since they add the same things (bob's only up to tier 4, extended vanilla up to tier 6). Bob's makes more sense to run with the rest of the bob mods suite, while extended vanilla is better suited to running standalone (with or without the rest of the extended vanilla suite)