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In this context, the word "desktop" refers not to the computer as a whole, but rather the user's home screen which Windows calls the desktop where one saves files that are regularly used or shortcuts to files and programs.
Which one would you say is, or feels, correct?
The file is in the desktop.
The file is on the desktop.
Glorfindel's answer is good! But my two cents...
The things that are 'as given' are considered on the 'surface' of the screen and thus, they are 'on the desktop/screen'. The folders are on the screen but to go into* the folder, you need to click it. It's not 'as is'. Hence, something 'in a folder'.
Another concept is, the thing that has 'no boundary' has something 'on' it. But if there's a boundary--say in a photo--it's 'in'. A photo 'on' the desktop; The car 'in' the photo.
I'd go for 'on the desktop', because the desktop is a metaphor for the old writing desks. You can store items in the writing desk of course, but then they're hidden.
Another possibility is 'The file is in the Desktop folder.'
