Wildfly Arquillian should be updated to use Arq. core 1.4.0 (recently released).
Ever since one particular change in WF Arq., there can be intermittent failures with tests that use WF Arq. and exception transformers. The commit introduced slightly different exception thrown when deployment fails.

This is not fault of WF Arq., it merely exposed a glitch in Arq. core.
The bug only manifests sometimes (I found it when upgrading WF Arq. in Weld and running CDI TCK which has loads of expected exceptions going through exception transformers) because it is dependent on the ordering of (3) Arq. interceptors. In some cases it may happen that transformers get null value instead of actual exception which then leads to misinterpreted test results.

Arq. issue - https://issues.jboss.org/browse/ARQ-2175