Say you have dependency A which transitively brings in dependency B with version 1 and you override the version of B to 2 via dependencyManagement, then m2repo contains B version 1 and version 2.
I would expect only version 2 to be included as this is what happens when you build a regular war-file (without swarm-plugin). This is also backed by mvn dependency:tree as this only shows version 2.
Add a explicit dependency to B (within dependencies, outside of dependencyManagement).
Note: This workaround will run into
SWARM-1009, B will be included twice.
I will come up with a showcase project on github ASAP.