I do that to work with the file. I Have been doing it as long as there has been a dock (OS X .....14 years?) and have never had this problem.
After I am finished with the file or folder (reading, copying info, unzipping (automatically), etc., then I move the file to where I want it.
If I need to refer to it additionally in the near future, I make an alias for the desktop.
I have been very busy lately and have quite a few files on the desktop (about 100 - mostly aliases) and I need to work on reducing them.
I thought maybe there was a corruption in some underthehood files (preferences ???) for the desktop or dock.
I run Disk Utility fairly often (and only have to repair permissions occasionally) usually before a backup.
Once again, Thank you rkaufmann87!