To reproduce this bug easily use two large file (I used ISO's):

1.) Create a directory called 'test'
2.) Copy (by clicking and dragging while holding down Ctrl) one large file (in my case oneiric-desktop-i386.iso) to the directory 'test'
3.) Wait for oneiric-desktop-i386.iso to transfer over
4.) Select the copy of oneiric-desktop-i386.iso that isn't in 'test' and one other file (in my case ubuntu-11.04-server-amd64.iso) and copy by Ctrl+dragging them to 'test'
5.) Observe the 'File Conflict' dialog. This has correct info ("Replace 'oneiric-desktop-i386.iso'?" and then gives the size of oneiric-desktop-i386.iso)
6.) Click the 'Skip' button
7.) Observe the file copy dialog. It says 'copying 2 files' and gives the progress in terms of the size of both files (1.4GB in this case). It should only say it's copying 1 file and give the size of it, as the other file has been skipped.

At least this is my take on it. It should be noted that also the transfer stops halfway through (once the unskipped file has been copied).