With additional testing, I think I've found the pattern. It's quite simple, brewing stands now use two hopper inputs. A hopper from the side can input bottles, and a hopper from the top can input potion ingredients. This appears to be intended behavior, so I don't think this is actually a bug.
+1 confirmed. Interestingly, hoppers can still put items into brewing stands from the side, but not from above. Perhaps this is intentional (though it would seem a little odd if it was)?
Jake King
With additional testing, I think I've found the pattern. It's quite simple, brewing stands now use two hopper inputs. A hopper from the side can input bottles, and a hopper from the top can input potion ingredients. This appears to be intended behavior, so I don't think this is actually a bug.