One of two things. It could be an accidental tape anomaly that the Floyd never noticed when they recorded the song, or they did, but it was so faint that they didn't care anymore, or perhaps it happened long after the tape was finished and the master just got damaged. In any event, if you listen very closely to the end of the song, you can hear the last low note sort of "burp" a bit.
Others have argued that Pink Floyd are too much of a purist in terms of their work and would never have allowed a glitch like that to be distributed without having some reason.
Lately is has been pointed out to me that the glitch occurs at what was originally the end of the first side. It could have been there to remind all the stoned listeners out there that it was time to turn the record :)
What the real reason is, however, is anybody's guess.