Reproducible locally by using Weld SE and adding any MR JAR with explicit bean discovery. For instance SR CP 1.0.20.
Similar situation could happen with annotated discovery, given that you have different beans for different JDK versions.
One such reproducer can be seen on my branch - https://github.com/manovotn/core/tree/weld2652_reproducer
Not that this is not an automated test, you need to inspect the logs to see INFO there since Weld is able bootstrap despite not being able to load these classes.
The logging looks something like this:
What happens is that Weld tries to load classes located under META-INF/versions which blows up as those classes should not be loaded directly. If I understand it correctly, using something like ClassLoader.loadClass(...) should already attempt to load proper version of any given class WRT Java version. Therefore, we should be good ignoring classes under META-INF/versions and simply avoid trying to load them.