I just had a similar problem. For six days in a row, one of my projects had each file downloaded exactly once, then it stopped. But the page did get 1-2 visits per day during this time, except for one day when there were none. Weird.
Maybe the Itch app tried to update it, and failed, but it counted as a download. I assume the app does not visit the page as a view, but as a download. Or the user clicking on update and cancelling it.
One or two users in an area that has connection issues might be enough for such a scenario. If the users manually cancels for whatever reason, that should also do the trick.
And if you download from the download page directly - if that does not count as a page view - connection issues also could explain this. Like only having a very slow connection and the user aborting because of that.
tl;dr Incomplete downloads count as downloads, afaik