I’ve recently played through some rather old modules (AL1: Siege of Shadowdale, AL2: Crimson Tides of Tethyr, Saleron’s Gambit - Chapter One) and in all of them there was an incident were a NPC was duplicated, quite obviously not on purpose. Instead of one character as described in the story, they were identical twins (in AL1 it was the post-final boss, in AL2 it was my companion, in SG it was the town wizard’s fairy companion).
I played AL1 and AL2 with NWN Diamond and SG with NWN:EE, so the issue doesn’t seem to be dependent on the edition, neither caused nor fixed by the EE, and these are three different modules by competent authors, so I assume it’s not an in-built error either. It’s also not completely predictable, since in the case of AL2, reloading a state before the twin popped up helped me to get rid of it (at least on the second try), so it seems like there’s a certain chance of this to happen but no guarantee.
Has that ever happened to others here as well? Is it a known issue with older, e.g. pre-1.69 modules? Or a glitch in NWN in general?
It’s not a glitch with NWN1 in general.
Sometimes authors choose to have two versions of a creature, in order to save scripting effort.
For example, in the very early days, it was the official method for levelling up henchmen (which is no longer necessary).
However, I’ve learned the hard way that the safest approach by far is to stick with one instance, and script it correctly. The closer the data model is to the entities depicted, the more likely it is to behave. There are exceptional cases, where trickery makes difficult things easier, but they’re always risky.
What you’re seeing is the result of script glitches which easily occur with duplicates.
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I see. Thanks for enlightening me! 
(Although it’s weird that the insignificant pixie in SG1 or the simple once-only encounter with the post-final boss in AL1 would even need duplicates. But who knows.)
Weird stuff happens for many reasons e.g. objects placed for testing then not removed.
For example, even in the OC, after all these years, one of the dragon caves contains a duplicate of the giant’s head that the dragon asks you to obtain as proof.