One episode, the Cutiemark Crusaders decided to ditch their sleepover at Fluttershy's to go look for her runaway chicken in the Everfree Forest in the middle of the night. Scootaloo get into an argument with Applebloom how a chickencall would sound like, so Applebloom goes "Yer right. It should be more like "Scoot-Scoot-Scootaloo!" and thus the joke was born to call Scootaloo a chicken, especially with her lacking ability to fly.