If it shows ? on a download, it's usually because the website has not told your browser the size of the file.
The website has began to feed data to your computer, but does not actually tell your computer HOW MUCH it is going to give. You will only know when it's done if; you already know the size of the file, or if you wait until it's done.
If it does this for everything though, could indicate a bug. Try rebooting your computer, relaunching Safari, or last case scenario, delete safari preferences by:
Open a Finder window, in the menu bar, click Go, hold alt/opt on the keyboard and choose "Library". Navigate to Caches and trash "com.apple.Safari". Go back up to Library and navigate to "Preferences", and trash "com.apple.Safari.plist" and any files with extra letters on the end (eg. "com.apple.Safari.plist.EntXCKM"). ONLY TRASH THE SAFARI ONES.