Just like the subject said, it is the tower sounds. They are messed up. Anything that has to do with the tower and sound is always glitching in and out. Mainly happens with anything that has to do with the items and the people like vangard, crucible, etc when you hold square to approach.
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Same thing happens to me. Decrypting engrams is most noticeable, 1 in 5 makes the sound.