I personally don't think it's a Weld problem, but you can try to enable debug log level for Weld in WF - see Weld: Documentation. Maybe you can describe your app little bit more. It is vanilla WildFly 12.0.0.Final right?
Maybe this is related to Hibernate [HV-1410] CDI Integration uses deprecated API - Hibernate JIRA .
Yes this is a vanilla WildFly 12.0.0.Final started with standalone-full.xml configuration. The database is Oracle Database 11g Express Edition Release 126.96.36.199.0 - 64bit
The OS is openSUSE Leap 42.3 with kernel 4.4.120-45.
The application is more a proof of concept which I took from https://blog.holisticon.de/wp-content/uploads/2011/10/ticket2rock-2.0-dist.zip
This application should cover all aspects of JEE. It was developped and tested under JBoss 6.1.0 Final. l migrated the application to WildFly.
I'm having exactly the same warnings that you've, when I deploy my application in Wildfly 12.0.0.Final. However, I think that the error that you're getting has no relation with that warnings. Because my application is deployed well, without any error.
My application uses JPA, EJB and servlets, just for the record.