Sometimes it's politics. Sometimes the lable pushes to not include the song on the album, sometimes the lyrical content isn't something the label wants (for instance, maybe someone would have thought "Ms. Holy Roller" was 2 aggressive and kept it off the album), and sometimes the label of the guest artist can keep the track off the album.
One thing that nobody knows, but i do cuz of connections, is that "Pump Me Up" waz originally intended for Big Willie Style, but Jazzy sampled so many things in the original version that they couldn't clear all the samples. The version of "Pump Me Up" on Willennium has fewer samples and apparently is pretty different from the version they recorded for Big Willie Style. That would be a situation where clearing samples kept a song off the album.