|They may very well be temp files and I don't think you can stop the system from creating them.|
The real question may be "Why isn't the app that created them deleting them after their purpose has been served?"
For example, if I open a Word doc, such as MyDoc.doc, Word will create a file called something like ~$yDoc.doc in the same directory. However, when I close the document, Word is supposed to erase the temp file. It doesn't always happen and some apps are better at it than others.
It might help if you knew which app was creating the files.