Iirc all scenarios have variable rewards based on how well you did, and one of the variable rewards is getting 2 modules (maybe even 3, I forget) instead of 1.
"How well you did" on the prison one is perhaps more obvious than others, but on the dyson one it depends on how many gatlings you killed, and on a lot of the others it depends on how quickly you win. On the ravenous shadow one it depends partly on how many enclaves survive and partly on how many bases survive.