With respect to PDB alternate location identifiers, an atom with two or more alternate locations read from a PDB file in PyMOL is treated as two or more independent atoms. Both atoms are a member of the associated residue and thus there will be extra (nonphysical) bonds present.
The easiest way to eliminate alterate conformations is to issue:
remove not alt ''+A alter all, alt=''
which will remove the alternate conformations and clear the alternate location identifiers.