The answer is yes to everything.
The reason Bug Buzz passed the Substitute is because as of Generation 6, sound based moves like Bug Buzz have the ability to pass Substitutes. The situation with Thunderbolt depend on your opponent. If your opponent had the ability Infiltrator, then the Substitute bypass was normal (Infiltrator lets you do that in Gen 6 as well). If not, then I'd require more information to identify if that was a bug or something normal.
And as for the list, here you go, Bulbapedia's got you covered. It says Gen 5, but the list didn't change in Gen 6 (apart from sound moves and Infiltrator) so it still applies for X and Yc