Update:
I tried to reproduce the bug and found out that if I place a flare on a block and then dismantle it with the pickarang (Quark), the flare gets no NBT Tag after getting assigned an empty one through the offhand.
I have the problem that when I have flares or blocks to build in my offhand, they seem to be assigned an NBT tag, so I can't stack them with other flares or blocks.