This issue is also is listed in the known issues thread found here
We are aware of an issue that is causing players to sometimes not receive credit for completing Junkenstein’s Revenge challenges. The team is actively working on a fix for this issue, which we expect to deploy in our next update. Until that time, we recommend supplementing your games played by playing additional matches in other modes.
We are working on a solution to ensure that all affected players receive their event rewards.