In the beginning when Jay and Silent Bob are in the 1970's, Jay's mom goes into the Record store (RST Video to be) and a Free Willy video is visible just inside the door, a movie that wasn't released until 1993.
When Jay and Silent Bob catch a ride in the van, Brent touches Justice's leg. Brent is first seen to move his left hand, but in the next shot we see his right hand on Justice's leg. We then see him retract his left hand again in the following shot.
When Brodie is restocking the comics and talking to Jay and Silent Bob in Brodie's Secret Stash, a guy is standing there reading a comic book. In the next shot, he is standing there with his arms closed. There was a shot in between where Brodie slaps the comic book out of the guy's hands because he is damaging the spine, but it was cut.
When Brodie shows Jay and Silent Bob the 'Bluntman & Chronic' article in Wizard magazine, there is a picture of Holden and Banky (obviously lifted from the DVD cover of Chasing Amy) but when Jay and Bob take the magazine to Holden's apartment the picture on the inside has changed to a still image from Chasing Amy.
When Jay and Silent Bob are beating up the clerk at a store at the end of the movie, they hit him and a sign falls down onto the counter. In the next shot, the sign is gone. In the third shot, the sign returns.
When Jay and Silent Bob are running from the security guards from the "Good Will Hunting 2: Hunting Season" set, Jay has his yellow jacket tied around his waist. But in the next shoot, where they are in the "Scream" set with Shannen Doherty, Jay has his yellow jacket on.
In Brodie's Secret Stash, Brody stands facing Jay and Bob, but the same comic, "Cable", as well as those around it, is behind all of them. It is unlikely the exact layout on the racks would be duplicated so close to each other, and no copies could be seen as Brody was walking backwards, placing comics in the rack.
After Jay and Silent Bob escape into the sewer pipe in Utah and make it to the end of the line at the dam, two things occur once they climb to the top: 1. There is no water on the other side (mountains can actually be seen), and 2. The background on the waterfall side of the dam is of the mountain face of Pyramid Lake, just north of Castaic, California, named for the way the cut out face looks like a pyramid. This would mean that the pipeline ran all the way from Utah to California and that they made it in the same day on foot.
The girls say they are from the University of Kansas and on their way to Colorado for the protest/break-in, but an earlier scene before Jay & Silent Bob go into the Mooby's (and meet Justice) shows that they are in Kansas City, MO. The University of Kansas is in Lawrence, KS, over two hours west of KCMO, so going to Kansas City would have been completely out of the way.
After the animal rescue, the van that Jay and Silent Bob traveled in blows up. You can clearly see the van door get blown off and then hit an invisible wall and bounce back rather than hit the police car that is parked next to it.
When Holden shows Jay and Silent Bob a web site in which anonymous film geeks trash their names, the page's address is seen, and it starts with "file:///Macintosh%..." rather than "http://", meaning that the page is coming directly from that computer, not the Internet.