Pepito sneaking up on Bud, while his hair resembled a shark fin, is a reference to the iconic scene from the famous film Jaws.
The joke about Rosa Parks moving to the back of her grave is a reference to how she was expected to move to the back of the bus, simply for being black.
Bud doesn't know the English translation of La Bamba, and apparently thinks "La" translates to "Planecrash". In actuality, "La" means "The" and "Bamba" is a made-up word, which is just the name of the dance that's intended to accompany the song.
Bud tells Becky, he's sick of her pointing out the plotholes in NCIS. Becky tells him that the real-life Navy doesn't actually investigate the kinds of crimes they do in the show. She's actually right about this, and most likely many more things, as that show relies a lot on suspension of disbelief in order for most of their storylines and premises to work.
When the aliens texted Bryce, their profile picture was shown to be one of the aliens from the 90's video game, Galaga.
Ernesto says "Bud's people" put a midget on Game of Thrones. This is a reference to the Caucasian character, Tyrion Lannister, who had actually been there since the first episode of the first season, so I have no idea why Ernesto implied he was "put" on the show.