steps

Create project:

build.sbt:

scalaVersion := "2.13.0"
cleanFiles += managedDirectory.value
managedDirectory := baseDirectory.value / "libs"
retrieveManaged := true
useCoursier := true // set explicitly for clarity

project/build.properties:

sbt.version=1.3.0

Test.scala:

object Test

Run:

sbt clean compile

problem

dependencies are not copied to managedDirectory, retrieveManaged stopped working in case of useCoursier := true

expectation

dependencies are copied to managedDirectory

notes

setting useCoursier := false or falling back to sbt 1.2.8 fixes the problem of course