Setting the ContainerMinSize has no impact when the the window is floating. It doesn't matter the window is floating initially or docked initially. ContainerMinSize is respected when the window is docked. To reproduce simply set the ContainerMinSize on the tool window. This can be via xaml or code.
var toolWindow = new ToolWindow(ContentDockSite, "documentOutlineToolWindow", "Document Outline", null, new TextBlock { Text = "Hello World" });
toolWindow.DefaultDockSide = ActiproSoftware.Windows.Controls.Side.Right;
toolWindow.Name = "documentOutlineToolWindow";
toolWindow.ContainerMinSize = new Size(350, 500);
<docking:ToolWindow x:Name="documentOutlineToolWindow" TabText="Document Outline" Title="Document Outline"
ContainerMinSize="150, 300"
ContainerDockedSize="300,500"
Description="Displays the primary document's document outline">
<TextBox x:Name="documentOutlineTextBox" Grid.Row="1" BorderThickness="0" Text="(none)" AcceptsReturn="True" IsReadOnly="True"
FontSize="10" HorizontalScrollBarVisibility="Auto" VerticalScrollBarVisibility="Auto" />
</docking:ToolWindow>