We've recently changed the Bounty system to keep your progress towards the reward crate from the previous day, if not completed, to give players a chance to complete them the next day instead of starting all over again. All details about this can be found HERE.
Since your two primary bounties are different, it appears to be a different issue or none at all.
For example, you completed 3 one day and then 2 new ones the other day, which gives you the final reward crate. You can still complete the remaining 3 new ones the other day, which will count towards the next reward crate, but you won't be able to claim another reward crate the same day. In your example, it looks like you needed to complete one more Bounty to collect the crate and then completed the other 4 Bounties as well, which counted towards the next reward crate. Does that make sense to you?
Did you already claim your daily Bounty reward crate by any chance?