It isn’t commonly a stain or blemish (5)
I believe the answer is:
taint
This clue is a triple definition!
'it isn't commonly' is the first definition.
(I've seen this before)
'a stain' is the second definition.
(I've seen this before)
'or' acts as a link.
'blemish' is the third definition.
(I've seen this before)
(Other definitions for taint that I've seen before include "Corrupt" , "(Trace of) corruption" , "Sully, stain" , "Flaw in Titan" , "It isn't commonly" .)