Looking at this in 2011 and below I believe Manually Applied represents where templates were applied either at the time the agent was manually added to a group by being dragged and dropped on the group or by a template being manually applied to a group's agent using the apply button.
I had to dig as I use autojoin groups to populate groups where I am applying templates. To track this down look at the group membership of the agent and check each group for the template you want to remove. Switch the template to None and hit apply to force the change. down the the affected agents.
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