There currently is a bug, yes.
The mouseover tooltip that lists your top runs has been excluding runs that fail the timer. That is a display issue only. The rewards will be correct on Tuesday, and you do not need to beat the timer for your Mythic Keystone dungeon completions to count towards progress.
And that is a separate issue. There’s often a delay of a few minutes before the Great Vault UI updates to reflect a recent Mythic Keystone completion. While we look into that, we’ve found that logging out of WoW and back in will force it to update.