Audio problem: Before the trio crashed into the Daily Planet (just before the battle with Supes), they were heard flying outside the building. For 3 superbeings with the ability to fly unaided, they sure sound heckuva lot like jet-propelled aircrafts. Jet aircrafts are noisy because of their engines, but superpeople?
Audio problem: When the three villains fly after Superman, they all gather in a circle and one of them says "Wait there". It can't be Ursa because it is too deep and neither Zod's or Non's lips are moving so it is not them. So, who is it?
Audio problem: Trapped under the elevator, Lois says "Capital P" but she is not mouthing the word.
Audio problem: Most of the times when the French terrorists talk, their lips are not in synch or their mouths don't move.
Audio problem: In the Fortress of Solitude, when Superman kneels before Zod, we hear Lois sobbing, but her mouth and body don't move.
Audio problem: During the disappearing/reappearing scene, Superman grabs Zod's neck and cries "Wrong again, Zod!" but his mouth isn't moving.
Audio problem: When Ursa lifts the bus she mumbles and laughs, but her mouth is closed.
Audio problem: As Superman's mom speaks in the recording, the reflection immediately to the hologram's right appears slightly out of sync with the main image. Also, there's one word the image says that the reflection's mouth doesn't mimic.
Audio problem: When the villains are trapped in the Phantom Zone glass Zod cries out something against Jor-El, but his mouth isn't in sync with what he says.
Audio problem: In the prison, Lex tells an inmate he wants his Liberace record, to which he replies, "It has a scratch on it," but his lips don't match the audio. In the Donner version, it's revealed that the original audio was "Tonight?"
Audio problem: When Non is launched towards the Empire State a man says "Wow, home run!", but his lips are not in sync.
Audio problem: At the Eiffel Tower, after Lois asks the French officer if the terrorists have the proper equipment, his voice is heard but from a side view his mouth and jaw don't move.
Audio problem: When the villains blow the people back in Metropolis, all the ones near the KFC restaurant (the waitress, the guy in the phone booth and the couple) shout or make comments but their mouths either don't move or are not in synch.
Answer: Superman was be able to kiss Lois in such a way that the heightened emotion wiped out her memory of his identity. To answer your second question, even though Lois promised not to tell anyone, Superman decided he does not want even her to know his secret identity.
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