1.Finnwhich not knowing where the Pyramid was despite being there when it was opened 112 years ago.
2.Lee as an infant wearing something extremely similar to the headress (for lack of a better word) that Tina always wears.
3.Where Lee got the picture of Tina from.
4.Lee denying something he had already admitted to. In Skate or Die he didn't deny when Biffy said he was in love with Tina yet in The Cam-didate he said him and Tina were just 'freinds.
5.In Friday Night Bites when Lynch shows the photo of Lee and Brandy kissing their is something missing, Cam should be in the picture. Also the camera angle changes from Lynch taking the photo from behind in Skate or Die to side on in Friday Night Bites
6.I may have figured out how Biffy's parents got to Coral Grove. When Cassandra is talking to Kimmie outside where His Eminence is you can just see in the background what appears to be a helicopter.
7.The most confusing mystery is probably in episode 1 when the Tatzelwurm put the key in Lee's bag. It would have to have been after Cam switched it but why not just put it in the switched bag so Lee could get it sooner. Also, how could VP Victoria know that the Tatzelwurm took the second Key if it happened 112 years ago?
8.It seems that Lee's real mother can't be brainwashed. In Date with Destiny Lee tells Jenny to cover her ears but Sue Ping doesn't seem to. This would imply that Lee's being unable to be hyponotized comes from his mother's side of the family.
9. Where Finnwich got the Quadrocle from because Alexander Nigma took it with him when he opened the Pyramid.
10. Kimmie seems to be immune to the Prank Song in Date With Destiny, while she is wearing headphones presumably to block it out she becomes annoyed at something Cassandra says while the music is still playing
11. Holger being immune to the Prank Song in Mastermind, possibly because it is the original Prank Song which is less effective.
In Episode 32 "The Curse of Earl Nigma" the skill of Lee's opponent in the fencing raises the possability that it was The Serpent in disguise which considering his behaviour after that i wouldn't put it past him.
In Episode 27 "The Dance-Part 2" it is never explained why the Council had an interest in the brainwashing technique because 1. "MWF owns everything, all over the world"-Biffy and 2. His Eminence would surely have some knowledge of the Song.
Why did they deliberately make the Pyramid so difficult to open (assuming they did create them). It is somewhat implied that they didn't make the Pyramid ("But once we have them how are we going to open it? Our research shows you need an eclipse"-Wurst "Or someone who can replicate one"-His Eminence