Two different operating system users must exist; each user runs a different DB2 instances. You execute the db2stop command as one of the two DB2 instance owners. Since one owner does not have any rights (even at the OS level) to temper with the data and processes of the other instance, it would be interesting to know how exactly you could bring down both instances by just stopping one of them.
So could you tell us the usual stuff (platform, DB2 version) along with the exact steps you performed and how you verified that both instances are down?