Scootaloo has numerous problems with her reproductive, urinary, respiratory and digestive tracts, namely, some embryonic ducts not fusing properly. She was born with various epiglottal defects, which is problematic not just for biological reasons but causes problems in speaking as the Equestria language frequently features /ʡ/. Similarly, her (ndegesebaceous) gland, though functional, was underdeveloped. She was also born without a uvula. Most of her digestive tract is fine, however, the division between her jejunum and ileum was closed by a wall (I believe the difference is internal width and lymph node distribution) and the two instead merged at the jejunal atrium of the ividzukofirorocśaifnƥrek. She has uterus didelphys, and her urinary syster has similar problems. Both urethral sphincters were nonfunctional and only one kidney worked. Surgery was able to correct this, however, she was tube fed until she was three, padded until she was six and wet the bed until she was twelve. The problem with her flight is believed to be a similar duct fusing issue, though how pegasus flight works is at this point a complete mystery.
When she met Apple Bloom and Sweetie Belle she was just out of hospital following the latest bit of surgery.