I see empty spaces in Finder on OS X 10.9.4, exactly as on the picture. What does it mean? The spaces are in between the other icons, not at the end of the listing.
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This means there was an icon there, but it's been deleted/moved/etc and your current view doesn't do automatic sorting. Go to View → Clean Up By → Name to fix it just once now or press ⌘J to open View Options and set Sort By to Name to fix this now and in the future.