In a early setting after the first murders, Inspector Matt returns to the crime scene and is holding a Mag-Lite flashlight. While the flashlight became the number one flashlight of all police departments it wasn't offered for sale till 1979. Several years after the first Zodiac murders.
In the final scene that takes place in the Ace hardware store, the logos in the front half are period correct, but as the camera pans to the back half, the packages have the current ace logo and look that is much different from the logo used at the time.
The school bus used for the Vallejo School District has Budd wheels on the front axle. Trucks and buses for this period had split-ring Dayton wheels. Budd wheels would not become commonplace on school bus chassis until the late 70's.
During the stakeout, when the police surround the Mercury, there is a camera shot that is from the back seat, over the driver's right shoulder. In the upper left corner of the windshield, there is a clear plastic Valvoline oil change sticker. These stickers were not in existence in 1968.
When the Zodiac is narrating his letter after the Chief of Police invites him to write with more details of the earlier murders, his narration leaves out the word "very" before "very happy to supply even more material." that appears in the letter that he is narrating.