If it didn't added, then you have to replay level 5000 to get the badge. Also, check your setting got open the milestone badge or not. Restart your device and update your game may also help.
As you can see in this photo, level 12988 is definitely bugged. The left items in the square on the left-hand side show that 2 clear square have to be destroyed, but the question is where? I strongly demand they fix it at once and reimburse the cost I spent.