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I published an article last year. The work was done at my previous university, but I submitted when I was studying at my new university.

When I submitted, the journal took my current affiliation along with my past affiliation because I used the current institution's IP address, even though I put only the previous affiliation. This was an open access journal and my current university has a subscription policy. But when I asked one of the editors about the fees, he told me that it was free for me being the first time. But they took the current university address for the funding.

Is there any problem with that? Do the university check the article's details during payment? If this matters, what can I do now?

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There is nothing wrong with publishing a dual-affiliation paper. It happens often when a person conducts a piece of research at one institution but finishes writing it up at another institution. This is a genuine dual affiliation because writing is part of the scientific work.

That said, however, I am extremely suspicious of a journal that does not allow you to declare your own affiliation. Your description of that and other interactions leads me to question whether you are being scammed by a predatory publisher. I would strongly recommend evaluating the quality of the publication and making sure you actually want to publish with them.

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