Same strange ingot glitch being reported. I'll try and give any details I've encountered.
Snapping ingots in order (closest to furnace, middle, farthest; 1, 2, 3 from here on) seems to work consistently, though it's difficult to get them to snap in that fashion. If you snap them on opposite sides, leave them; moving either to 2 will likely turn that one into what I'll call a "ghost ingot". Ghost ingots can be hammered (silently), though they display very peculiar properties. I haven't noticed enough consistency to say for sure what's happening behind the scenes, though. The silent ingots do seem to add to the hidden counter; hammering a ghost ingot 7 times may not turn it into a dagger, and stacking three other ingots may make a greatsword on the first hit. It's very peculiar.
Moving ingots between the three slots seems to be the root cause of the issue. If I drop one on 1 and 3 and hammer them once, it plays the 2-ingot sound, and if I swap them, they both become ghost ingots. No sound when hammering. If I place another two ingots on slots 1 and 2, it plays the 2-ingot sound once again, and the 2 ghosts are restored to their usual sounds. I've noticed it's possible to have both ingots on the anvil treated as a pair of single ingots, and in general, removing a problem ingot for a forge or two should fix the problem. Rule of thumb: don't move the ingots.
Oh, and the telekinetic hammer bug, where hammering a heated ingot while another is on the forge will act like you hammered the one(s) on the forge. No matter the distance.