In Clarks dream sequence, the 2013 newspaper that Jeff Hage gives to Lois has an article about the recent deaths of Jason and Genevieve Teague, who both died May 18, 2005.
When Zod and Clark are fighting on the rooftop after the other Kryptonians have ascended, Zod's first slash at Clark with the blue kryptonite dagger leaves a diagonal cut across his chest although the swing was clearly horizontal from right to left.
When Lois' elbow breaks the glass of the phone booth, the CGI glass completely shatters and falls away. When the shot changes angles as Lois opens her eyes, most of the glass is intact with only a jagged hole missing.
After Zod throws Lois towards the phone booth and Clark uppercuts Zod and begins to run toward Lois, the broken pane of glass where her elbow strikes the phone booth can already be seen. When the camera changes angles and he has already caught her, the sound of glass shattering can then be heard.
The Kandorian that Tess "killed" in "Crossfire" re-appears as one of the many sent to New Krypton, and is next to Clark during this scene. He also seems to have recovered his dogtag, which contains no blood stains.
When Clark falls of the roof in the ending, he falls off twice.
When Clark opens the box from his mother containing "the suit", during his close up you see the superman shield reflected in his eyes. However if this was a true reflection, the symbol would be backwards.