What is the purpose of all the televisions in the castle?
Where is Lorenzo and Riccardo getting all their funding for creating experiments and ensuring the maintenance for the castle? I find it unlikely that they are getting money from legitimate means.
Okay, I know that this is secondary, but still: Daniella is shown cooking something that seems pasta but is implied to be the bloodied hair of Fiona's mother: How can you possibly pass hair (even if long and blonde) for spaghetti? One should be able to tell the difference on sight. And besides, putting the sauce... while the pasta is still boiling? Come on....
Having screwed up angel hair pasta myself, there's a very easy way to make that mistake: if you overcook it severely enough, and if the noodles are dark enough (ie, whole wheat or other alternative, and not semolina), they can bear a freaky resemblance when scooped up, especially if boiled in salt water to keep it from sticking. As to the sauce, it could have meant that the sauce was boiling, and not the water.
Well, in that case, still it puzzles me that what seems to be the main and only chef in such a big castle can do such a gross mess. On the other hand, it can be Fridge Brilliance considering that is doubtful that any of the residents of the castle actually cares about eating mere pasta...
How did Riccardo know to set up a pile of logs in the path of the Bellis' car? In fact, how could he have known they were passing through the area at all?
Doesn't he have some sort of paranormal powers?
The lyrics of Endless Zero imply that Ugo and Ayla had the same desire for Fiona's Azoth and immortality. It's possible they contacted them and were bringing Fiona back to the castle for harvesting, but were killed as a punishment for leaving in the first place.