Hi!
It’s because the taxonomy group logic is set to ‘OR’ instead of the default ‘AND’, you can change that here: http://i.imgur.com/lxNpWEl.png
The current configuration basically means, that ‘Display the results if any of team_department OR the team_designation filter matches.’
If you change that back to the default ‘AND’, then a result has to match both filters, if any of the values are checked.