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Interesting, this is usually done when you get to keep your passport while they process the application. But generally in these cases the embassy takes the precautionary step of stamping your passport with their seal to show the application was taken in for processing. This is so that they may identify whether or not this was the passport originally presented to them.
Weird, but I am assuming this was also the case here.
No need to worry about any issues, refusals are stored in the VIS. If they have any doubts they will consult the system and see you are clear. See the link for what is added to VIS file when you have a visa refused/granted.