Logical focus scopes do not work properly within dock sites. In the following sample, clicking on Button2 within ToolWindow2 causes ToolWindow2 to be deactivated and ToolWindow1 to be activated. Clicking on Button1 within ToolWindow1 does not cause this problem. I can "fix" the issue by removing the focus scope in ToolWindow2, but focus scopes should be compatible with dock sites. This seems to be a bug.
<docking:DockSite>
<docking:SplitContainer>
<docking:ToolWindowContainer>
<docking:ToolWindow Title="ToolWindow1">
<Button Content="Button1" />
</docking:ToolWindow>
</docking:ToolWindowContainer>
<docking:ToolWindowContainer>
<docking:ToolWindow Title="ToolWindow2">
<Border FocusManager.IsFocusScope="True">
<Button Content="Button2" />
</Border>
</docking:ToolWindow>
</docking:ToolWindowContainer>
</docking:SplitContainer>
</docking:DockSite>