Upon completing a room, if a room clear reward would spawn, another, different reward spawns next to it. If Isaac takes/opens one, the other disappears.
If one of the consumables generated by this effect is a heart, converting it with Apple of Sodom or Keeper will not cause the other consumable to disappear.
Dark Bum, Key Bum, Bum Friend, Bumbo, and the familiar gained from the Super Bum transformation will cause other items to disappear when they take their respective pickups.[1]
Magneto opening a chest does not make the other reward disappear. Picking up the other reward afterwards will only remove the empty chest, and picking up the contents of the chest will not make the other reward disappear, letting Isaac take both rewards. This does not apply to chests with items in them, which disappear or make the other reward disappear as normal.