When you upload a file to a Google Site, the spaces in filenames in the URLs used to be stripped. So if a user uploads "AB.gif" and "A B.gif", they were treated as the same and the second one would be uploaded as new version of the first rather than a different file - which was not ideal. This may not have been apparent because until recently, the spaces were still shown in the filenames as displayed by the user interface.
With the recent introduction of a new uploader, embedded spaces are now included in file's URL.
Unfortunately, this has the side effect that if previously you had uploaded a file called:
it was previously stored with the name
If you now upload the same file it will be stored as a completely new file
rather than a new version of the old file.
To make it clear to the user, the user interface now displays the filenames as they appear in the file's URL. So files that had filenames containing spaces that were uploaded prior to the introduction of a new file uploader will now be displayed without spaces since that is how they are (and always were) actually stored.