In the pilot, the geeks are shown playing basketball in a gym with very distinctive wood paneling. From episode 2 onward, the school gym no longer has wood paneling.
When Lindsay meets Daniel in the cafeteria, the sign behind them reads: "Do not place silverware in the trass". This could be intended to show that the lunch staffer was a poor speller or that a student messed with the sign's removable letters.
When Nick shows Lindsay his drum set, he states that he only needs a few more pieces and he'll have a bigger drum kit than Neil Peart of the band Rush. When he speaks of Neil he uses the common mispronunciation of his last name as to being "pert". Although a common mistake in real life, Neil's last name is actually pronounced "peert".
When the Weirs are having dinner, a plastic ketchup bottle of a type not used in 1980 can be seen on the table.