I don't think the "restoration" was done correctly.
I think that they used Time Machine to add ALL the pictures in your Time Machine files to the existing pictures on your Mac.
Correctly used, Time Machine can be used to replace missing pictures, by going back in time until the missing pictures are visible, or the entire library.
Take the iPhoto library and move it onto the desktop.
Keep the folder where your iPhoto library was, open
Launch Time Machine
It will show you the Time Machine version of that folder
Go back to a point that you know everything was organized, a couple of weeks maybe
Select the iPhoto Library and hit the Restore button
This will place the entire folder back in the place that it came from