Well, I had similar issue in my Download folder. Many times I got the message 'Startup Disk is almost full'. Finder was showing 37 GB in that folder, but, checking each subfolder individually, the size of all was like 10xc2xa0GB smaller.
So, I could not (yet) figure out why it happens, but, I could find out how to fix it.
The only matter is the problem may keep showing itself up.
So, to fix this, go to 'System Preferences' -> 'Spotlight', then, 'Privacy'.
Click on the '+' button, and add the disk which contains the 'wrong sized folder'. Hit OK for confirmation.
Reboot your Mac (when I learned about it, this step was not mentioned. I did it on my own, just to make sure).
After the reboot, go back to system 'System Preferences' -> 'Spotlight', then, 'Privacy'. Now, click in a disk you just added, and remove it (using the '-' button).
And it's done the trick.
PS 1: MacBook Air 2010, OSxc2xa0Xxc2xa0v10.8.5 (Mountain Lion), 256 GB SSD
PS 2: Sorry, I do not remember where I learned it, but, in the worst case, you will lose a bit of time while OSxc2xa0X rebuilds the file indexes to improve spotlight search.
PS 3: If you realize the spotlight is not searching how should be, it is a signal that above procedure should be executed.
PS 4: Another tip that may be helpful: Go to Disk Utility, select your disk, and hit 'verify disk permissions'. After done, click in 'repair disk permissions'.