I've found lately (for 2 weeks maybe) that extrabees, notably their alveary blocks, have a few problems. 1. Occasionally, these alveary blocks won't work. This problem can be fixed by resetting the alveary. (Breaking a block in it and replacing it, etc.) 2. Attempting to place anything except a frame for bees in the "Frame Housing" block will destroy it. (I've lost a thorns 2, protection 4 to this, due to accidentally shift-clicking the wrong item.) 3.Mutator blocks accept any item. (Not really a major bug at all.) There might actually be a few more that I'm overlooking. Maybe.
If you are 100% sure about these bugs, you're better to report them to binne on the ExtraBees thread. But apart from the the first one, i have not ever experienced those bugs first hand.