All printers apply the finishing option to the compiled job output, and the problem lies in that.
There are 2 ways the App can do it.
Host collation and Printer collation.
With Host collation, the application takes the job and puts the 2 separate pages together as one 2 page document. This is better on dumb printers like old ink jets that have no interpreter in them, but it sucks if the printer is more advanced, because the printer has no idea that there are 2 single page jobs, it only knows about one job with 2 pages.
With Printer collation, only one page gets sent, and it sends with a command to print it 2 times, so the printer knows it is 2 different jobs, and for that reason it won't duplex it (in your case) or staple it together (Excel is notorious for this one)
Adobe has a good article on it
Sometimes, in cases like yours, simply uncheck the box for collate can resolve the matter too (Collate means nothing to a single page job, obviously won't apply if multipage)
When printing multiple copies of a single page of a multi-page document, the printer is duplexing the copies together. They should remain single sheets, as they're separate copies. If I manually turn off duplexing, it'll print fine, but I shouldn't have to do that. It shouldn't be duplexing separate copies of a document together. Doesn't do this with single-page documents, even if duplexing is enabled.