It's not COMMON, but also not COMPLETELY unheard of, for two of Brian's sessions to have the same master #, even though the sessions were for completely different songs; for instance, we see this happening a couple of times in "The SMiLE Sessions", but the difference is the same TITLE was also used for both songs (for instance, the second version of CHILD IS FATHER OF THE MAN was logged as a CABIN ESSENCE session, both in title & master #, and WITH ME TONIGHT was logged as a VEGETABLES session, both in title & master #...that doesn't necessarily mean that those songs were intended to be part of one another, though...but it also doesn't mean they weren't...

).
But in the case of HERE TODAY and GOOD VIBRATIONS, I think we can see what happened: the first GOOD VIBES session was on February 17-18, and master # 55680 was used. GOOD VIBES was intended for the "Pet Sounds" album at this point. When the track that became HERE TODAY was cut, on March 11, no master # was indicatd on the AFM sheet, however master # 55680 was shifted over & reassiged to the new track when it was determined that GOOD VIBES would NOT be included on the album. When the next GOOD VIBES sesson rolled around, on April 9, a NEW master # (55949) was employed. That master # would change a couple of times over the course of the ensuing months, but the final GOOD VIBES tracking session on 9/1 utilized 55949 again.