Skin leaves a film of sweat and sebum, slightly acidic, that stays on the steel. On a gun that is handled and then put away without wiping, that film is enough to bring up rusty fingerprints within days, especially in hot, humid weather.
The right habit fits in one sentence: wipe the gun with a cloth before storing it, then run a very lightly oiled cloth over the metal parts you touched. There is no need to oil the whole gun every time you handle it, only the contact areas.
A closed case is a closed volume. The gun sometimes goes in still cold, after a car journey or an outdoor session: moisture from the air then condenses on the metal and stays trapped under the foam. That is the most common cause of rust discovered “for no reason”.
Let the gun come back to room temperature before storing it, and make sure the case is dry. A case that got wet on a trip is emptied, cleaned and fully dried before a gun goes back in.