Oh my goodness, I'm sorry for the bug. I tested the game extensively just for the possibility of returning to the old bakery (I ended up copying and editing the maps so they were "remade" to make it easier instead of just creating new maps) and never once caught that one. As for the second part... well, the story seemed incomplete without it because the main character wanted to find out why the manor was cursed at all. And I really wanted to portray what Cuppy really was meant to be.
The "Add ingredients" part was actually very hard to get to work; again, I tested that for over three hours and found SOME way to get it to work. The variables are SUPPOSED to clear if you don't have all of the ingredients so it doesn't duplicate anything, and it looked clear when I got it to actually work that way. You DO keep the items afterward, because they were meant to be used for other parts of the story, but I simply did not have the time to implement those parts. Clearing the evidence was supposed to change some of Heathcroft's and the guards' reactions; I did not have time to implement that, so for now it does nothing except give some flavor and allow the player to be a jerk if they wanted to. I'm not trying to excuse the mess, and I hope I don't come across that way. I simply ran out of time to make either of those things do anything.
Thank you for pointing this out. All I can say is that I'm sorry I didn't catch those bugs, and that some of what I had planned was cut because of how long my playthrough for it was becoming; I left in clearing up all of the evidence because it makes you wonder, a little bit, if the main character even understands what Cuppy wants him to do or if he's genuinely that clueless.