pacman has detected a file conflict, and by design, will not overwrite files for you. This is a design feature, not a flaw. It is the responsibility of the user - not the package manager - to maintain their system.
The issue is usually trivial to solve. A safe way is to first check if another package owns the file:
$ pacman -Qo /path/to/file
If the file is owned by another package - report it on our issue tracker.
If the file is not owned by another package - either rename or remove the file which already exists in the filesystem, and run
pacman -Syu again.
As always, make sure you read and follow the #news before attempting any upgrade.