Well, in the case of the Beatles, EMI and Parlophone were the Beatles English labels and Capital was their American label (until they incorporated and created their own label, Apple). At the time in Europe, leading singles weren't usually featured on LPs, while in America they were. As such, when the Beatles records were brought State Side, tracks were removed from the British release so the singles could be included on the LP. or, like in the case of Help!, to include George Martin's score from the movie. This is a general explanation and specific instances might have different explanations.

Edit: additionally, when bringing the Beatles over, capital wanted to release multiple Beatles albums at once, so there would be a large backlog and multiple record sales, so they took loose Beatles tracks that weren't on actual LPs, as well as songs that were on the UK releases, and released them as compilations like Yesterday and Today and Hey Jude.