From my understanding, Shazam can differentiate between songs that share samples by doing classification on a windowed section of input. I.e, take 5 seconds of recording, and classify on t=0..2, 1..3, 2..4, 3..5. The idea being that the sample usage won't continue forever, and you will eventually get a new pattern. (You can even use your classifications from t=0..2 as priors for future classifications!).

For an easy intro to how Shazam works, see this: https://www.toptal.com/algorithms/shazam-it-music-processing...