In ADOM 3.0.6, I did something like the following:
* had a few (+0, 1d4) rocks in the inventory,
* had unidentified rocks in the missile slot,
* picked up a few more (+0, 1d4) unpaid rocks in the shop,
* paid for them with $ command (funnily the shopkeeper was not in sight),
* had to use the missiles so that the rocks became identified.
Then, when the missiles from the missile slot got used, I got the error:
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Version 3.0.6 (Windows)
Error: Duplicate found while filtering item list (6 rocks (+0, 1d4)).
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I didn't look in the inventory to see when, if ever, the unpaid-turned-paid rocks merged with some other of my inventory rocks.
The B/U/C status of everything was unknown all the way.