Thanks to @ccxCZ on #[email protected], I could find what was the problem.
Using the following:
tmux show-options -g | grep prefix
Showed me that the prefix was:
prefix `
Testing it, it was indeed this. I don't know how it turned out this way.
Since my tmux.conf was right, I just had to do:
tmux source /etc/tmux.conf
And the prefix was set back to the right way.