Seam doesn't use WTP API to handle web.xml, but copy web.xml created by seam-gen.
It isn't compatble with any facet that updates web.xml (Seam's web.xml includes the JSF servlet and mapping, but overwrites the setting added by the dynamic web and JSF facet )
If the Seam facet is the last executed facet, Seam will overwrite artifacts added to the web.xml file by other facets (I get this issue when adding the new correct BIRT facet that doesn't depend on the Seam facet).
If some facet is executed after executing the Seam facet, it will overwrite Seam setting (I get this issue when adding the new BIRT facet that depends on the Seam facet).

You can test this by adding the Axis2 Web Service facet when creating a Seam project. AxisServlet, AxisAdminServlet and servlet mappings for these servlets won't be created (the Seam facet overwrites Axis2 setting).