I had a VS2008 project that was showing this warning, and I couldn't find a solution anywhere - perhaps my google-fu is weak.
In any case, the apparent solution to this is to make sure that the TagName is the name of control class.
So for my example, the following displayed the warning:
<%@ Register Src="~/path/to/Control.ascx" TagName="tagName" TagPrefix="tagprefix" %>
<tagprefix:tagName runat="server" id="controlID" />
But changing it to:
<%@ Register Src="~/path/to/Control.ascx" TagName="Control" TagPrefix="tagprefix" %>
<tagprefix:Control runat="server" id="controlID" />
fixes it.
YMMV.