I've always thought Bono said "You wanted violence, and you got nearer" instead of "You wanted violins, and you got Nero" in Mercy.
"On a Jersey car" (whatever that means) / "I'm a traffic cop" in NLOTH.
"Just a start, til we die, you and I will break a fight" (my imagination at work) / "Justified, til we die, you and I will magnify" in Magnificent.
"Sleep comes like a drill" in In God's Country.
"And I would chase you down again" / "And I would chase you down the wind" in Wild Honey.
"Dressed up, like a cockroach" / "Dressed up, like a car crash" in Stay.
I'm pretty sure there are many, many more that I can't remember now. I'm always making up new lyrics!