I was under the impression that this was one of the issues that got fixed with 0.6, and indeed went awhile before it came up… sadly, it still seems to be around, and is still related to repeat-crafting of liquids, like boiling water. Essentially, I’ve got a stack of water bottles that I fill by boiling rainwater. I didn’t notice anything was wrong until it started repeatedly failing to accept input (“pour the drink you just crafted on the ground instead of storing it? no? okay, I’ll just disintegrate it instead.”), screenshots reveal that yeah, the fulls and the empties were somehow on the same letter (‘a’), yet nonfunctionally pretending to be on a different letter for the purpose of accepting input.
Related: saying ‘no’ to pouring a liquid on the ground should return you to the select a container prompt, rather than disintegrating the liquid in question.