Actor Allusion: A possibly unintentional one. At one point, Danny (played by Scott Menville) shouts, "Way to go, Rainbow! All right!", referring to the Rainbow of Light that was fighting the Smooze. At around the same time, he had previously played a character named Brian, who was friends with a certain character called "Rainbow". One wonders if this line had been taken from either the specials or TV seriesnote both of which were made by a rival production company, and based on a rival franchise. (since Brian clearly didn't say that line in the movienote Which was also made by DIC).
Irony as She Is Cast: After hearing the part of "I'll Go It Alone" where Baby Lickety Split and Spike start trying to sing high notes but just come off as screaming, most people have assumed that Baby Lickety Split has no hope in the music business. In real life, her voice actress, Alice Playten, has done work on Broadway and actually has something of a nice voice.
It should be said that this would have been a little confusing to the target audience the first time they saw the film... and totally awesome upon rewatching it as an adult.
As for why the scenes were cut...well, considering the aforementioned G.I. Joe scene involved a drunk Shipwreck seeing one of the ponies while drinking, before proceeding to smash his whiskey bottle and start praying to himself, it's no small wonder Hasbro refused. Their exact response? "Very funny... no".