I'm doing some sanity checking on an LDAP database in preparation for a version upgrade on our LDAP server, and I came upon a very few users sharing the same sambaSID
attribute. I wonder if I should be concerned about it? And, if yes, what would be the easiest way to solve the problem?
This is something you should be concerned about. In pure Microsoft networks a duplicate SID should never occur, as that's the primary-key that AD uses to determine which objects are which. Since this attribute is used by Samba operating in PDC mode while using LDAP as a back-end, Windows servers attempting to translate a SID into an object name will get inconsistent results for those objects.
Fixing it is a four step process.
Step 2 is the hardest by far. The complexity of your environment will determine how much pain it will cause to dig into. On Linux systems you may be able to dig filesystems looking for the right Owner information, as that may be set independently of the SID lookup. Your Windows systems are going to be a lot harder.