This is one Mac OS X behavior every new Mac users must keep in mind, especially for those coming from Windows: when you copy/move a folder to a location containing a folder with the same name, Mac OS X will replace the entire content of the folder with the new one you are copying/moving over. Under Windows, the files under the two folders will be merged together.
Let say you have five photos under your folder ~/Pictures/Photos/ with the file names feb001.jpg, feb002.jpg, feb003.jpg, feb004.jpg and feb005.jpg. And on your USB thumbdrive you have a folder named Photos which has three photos with the file names feb004.jpg, feb005.jpg and feb006.jpg.
Under Mac OS X, when you copy the Photos folder from your USB thumbdrive to your ~/Pictures folder, the system will prompt you to confirm. If you proceed by clicking on the “Replace” button, the ~/Pictures/Photos content will be replaced by the content on your thumbdrive, thus you will have the files feb004.jpg, feb005.jpg and feb006.jpg. Files feb001.jpg, feb002.jpg and feb003.jpg are gone!
Under Windows, system will merge the contents of the two folders, result in six files feb001.jpg to feb006.jpg. Files feb004.jpg and feb005.jpg will be overwritten with the version on the USB thumbdrive.
As you can see this OS X behaviour can be damaging if you are not being careful, imagine having your whole year’s photos wipe out by a folder copy.