Are you using IntegrationTest configuration in SBT?
I had the same problem and finally it was solved by adding:
(managedClasspath in IntegrationTest) += (packageBin in Assets).value
in my build.sbt
It may not be the same for you, but I use Gulp to create my css and js files and put them in the "out" directory. Therefore, to get them from the assembly, I also had to add:
unmanagedResourceDirectories in Assets <+= baseDirectory { _ / "out" }
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