Not only when you are deleting
I was sorting through my photos when I discovered this bug. If you move files to another folder, the cover flow gets out of sync the same way it does when you are deleting files. If you expand and collapse any folder, it forces the cover flow to re-sync. Just clicking another item doesn't change anything. Selecting a file in the other end of the list does not change anything either.
To any developer reading this thread, what happens is the following:
Say you have a list of files numbered from 1 and onward.
If you delete (or move) a file, an operation that will remove the file from the list of files in finder, it does NOT remove the same file from the cover flow. Causing an off-by-one correlation between the name of the files in the file list, and the files in the cover flow.
If you delete file number 1.
(File List) : (Cover Flow)
File name 2 has cover from file name 1
File name 3 has cover from file name 2
et cetera...
If you move or delete multiple files, for instance 5 files, the gap is 5 instead of 1, so it seems to me like a simple remove-from-one-list (the list of files), forget-to-remove-from-the-other-list (coverflow) kind of bug.
To people saying that this problem is not serious: If it causes users to unknowingly delete files they don't want to delete, it is seriously enough.