This only happens when I use autorename_workspaces.py (I could not reproduce it whit i3-msg rename ...):
When I use a dual monitor setup (I usually have my laptop screen below an hdmi-connected one) and I move my mouse from the laptop screen to the external screen with focus_follows_mouse enabled the leftmost workspace (with the lowest number) on the external screen gets selected (only happens then!! It does not when I use keyboard shortcuts/commands like $mod+up or i3-msg focus output HDMI1 ).
This is really irritating and I have no idea why this happens. Right now I always have to keep my most important window as the one with the lowest number, to prevent this issue.