I'd found a number of bugs in a project binary I had just uploaded, and so I decided to delete and reupload a fixed version of the binary. However, my reuploaded version would not show up in the project's download list unless it was saved with a different name than the file I had deleted.
The project's download page is here: http://bitbucket.org/alunbestor/boxer/downloads
You'll note that the number in the downloads tab is 15, but there are only 11 files listed for download. The missing files are there on the server - I can download them directly by entering their expected URL - but they don't show up in the list. It looks to me like "deleted" files are being hidden, not deleted, and uploading a new version with the same name replaces the old file but doesn't unhide it in the process.
<<issue 1942>> may be related to this.