The real animals were paired two-by-two, but many of them were actually same-sex couples. This was for safety: a bull elephant was considered a safety risk so two females were used. With giraffes, males can be friendly. Pairs of male giraffes were used.
The American Humane Society oversaw the one hundred species of animals that were used in the film. In scenes including both predators and prey, the animals were digitally added, to ensure their safety.
(at around 17 mins) When God appears to Evan in the back of his SUV, Evan screams, and God replies "Let it out, son. It's the beginning of wisdom." This is a paraphrase of Proverbs 1:7: "The fear of the LORD is the beginning of knowledge: but fools despise wisdom and instruction."
Like the studio version of the Titanic (1997), the Ark was only finished on one side. While the starboard side had hull-planking and painted detail, the port side was left rough.
(at around 1h) When God takes the form of a waiter, the name tag on his shirt reads "Al Mighty".
Catherine Bell: (at around 1 min) At the beginning, Catherine Bell reprises her role of Susan Ortega, Evan's co-anchor in Bruce Almighty (2003). She is uncredited, and only appears briefly.