The death of Scootaloo's mother. Heck, that entire story arc was part CMOH, part Tearjerker as we see both how much Firefly loved her daughter and how much she wanted to be there for her, but couldn't.
Sandy's outburst over her frustration about how time travel can't save the life of Firefly, Scootaloo's mother and Sandy's dear friend.
here, where it at first seems that, in a Hope Spot,Sandy has found a safe home, only to believe it isn't. It quickly turns into a CMOA and a CMOH when the Doctor reassures her and convinces Twilight and Sandysayinghe will protect them, shaking off his Discording in the process.
Scootaloo failing the flight examseems like it at first, but it is subverted (turning into a CMOA) when Factory reveals that the test was for pegasi FOUR YEARS OLDER, and Scootaloo did BETTER than the average for her age.
Factory saying she shouldn't use her scooter as much though is a bit sad (though Word of God says we'll probably see it again).