I created a simple GitHub project (branch moduleClash) which can simulate this problem.
Its an SE application which (for reasons unknown) decides to extends org.jboss.weld.environment.ContainerContext while using modular system in JDK 9.

Now, this happens if you depend on relevant Weld part (servlet-core here, as that depends on weld-environment-common) AND IN THE SAME TIME have this Weld jar added on module path (not class path). The reason being that this way Maven will force the creation of so called automatic modules out of Weld dependencies. If you added the jar on a classpath instead, this should work, but as of now, I am unable to convince Maven to do just that :-/

Also, I cannot really say if this would be a blocker if we were to modularize Weld (which I unsure we aim to, at least any time soon^TM^), but it might prove to be so.
I'll just keep poking my nose into this a while longer.