A file 'A' has a material node 'X', and a file 'B' has a different material node but also named 'X'.
Issue occur in a file C, when both of these materials are linked to common file.
Update:
There is even a bigger problem. If 2 group instances are linked to the same file, and an object within first group instance has the same name as another object in second group instance, one of these two won't be visible during rendering.
A file 'A' has a material node 'X', and a file 'B' has a different material node but also named 'X'. Issue occur in a file C, when both of these materials are linked to common file.
Update: There is even a bigger problem. If 2 group instances are linked to the same file, and an object within first group instance has the same name as another object in second group instance, one of these two won't be visible during rendering.