Hoppers try to insert items into the output-slot of the fusion reactors built-in breeding reactor, instead of it's input-slot.
They will also try to take items out of the input-slot rather than the output-slot. (the fusion byproduct (ionized particles / Chlorophyte / etc.) will still get extracted correctly)
This prevents automation of the fusion reactors breeding reactor.
This also applies to conveyors and item-transport-blocks from other mods.
This also happens when NTM is the only mod running.
I am using forge version 14.23.5.2860 (latest 1.12.2), NTM Extended version 2.0.2 and Java 8 for testing.