Broken Base: Before the advent of version 5, there was a sharp divide between which versions to use. Some stuck to vanilla 3.9, others preferred 3.9 with the 3.9+ mod. Others preferred 3.95. In the Groove fans stuck to OpenITG. A small contingent preferred 4.x. However, since the creation of sm-ssc (and it becoming SM5), this divide isn't as pronounced as it once was.
Dork Age: The 4.x builds. They never reached widespread adoption since they were rather buggy and unstable, and most of the community stuck to using the 3.9 build (and the 3.9+ mod) or the sm-ssc fork. Fortunately, things have since picked up, with sm-ssc being merged into the main repository as version 5.x (and the opening of a GitHub, with the sm-ssc team now spearheading the development of the game.
Fandom Rivalry: With osu! , mainly due to the game pandering to anime fans (which Stepmaina already does with the Otaku Dreams packs), being much more popular and OsuMania practically being a broken knock off of Stepmania proper.
Game-Breaking Bug: The Assist Tick bug, which will crash Stempania if you have the assist tick on in the editor and you stop testing a chart. Happens randomly too, and only in the mode people would use the assist tick.
Sometimes editing in 5 can glitch out on playback and not play the audio.
Ironically, the only reason it was patched out was because it messes with scoring. The update immediately after the above adds a much easier to use variant that also plays nice with the scoring system.