Searched the forums to come and report exactly this. Made a reply in the separate thread reporting the bug for Wolf Howl. Managed to receive the 50 Creds for Duplicate Protection on the Protosomid Shoulder Guard, but failed to receive the 50 Creds for the Emissary Operator Collection, as the OP stated. Note that I am experiencing these discrepancies on PC. Have screenshots of Reaching Nightwave Reward Tiers both before and after these milestones reflecting the failure in appropriate cred rewards and can post if necessary.