when is it adding thses numbers? When you are saving the files? On Macs if you try to save a file with the same name, the OS will append a number after the name. In Filemaker there is no need to "save" a file unless it is for back up purposes (which you should do, but give it a different name) as the file updates itself every time you commit any changes. You can simply close the file and when you reopen it, go right back to where you left off.
Note: if there is a start up script you may get redirected to the "home screen" rather than go back to where you were when you closed the file.
What are you looking at when you see these numbers?