[error] a required artifact is not listed by module descriptor: *#*!*.*

When I link my projects together in a certain way, sbt produces this error when running sbt eclipse.

[info] About to create Eclipse project files for your project(s).
[error] a required artifact is not listed by module descriptor: *#*!*.*
[error] a required artifact is not listed by module descriptor: *#*!*.*
[error] a required artifact is not listed by module descriptor: *#*!*.*
[error] a required artifact is not listed by module descriptor: *#*!*.*
[error] a required artifact is not listed by module descriptor: *#*!*.*
[error] a required artifact is not listed by module descriptor: *#*!*.*
...

Everything else works fine, compiling, building assemblies,... Even the project generation doesn't seem to suffer.

One special thing about the projects is that they transitively depend on other modules in the project.

Say my project has 5 modules, mA, mB, mC, mD, mE.
And one extnernal dependency (which can be used both as a source as a binary dependency) d1.

They depend like this.

mA <- mB <- mC <- mD -
       ^     ` <- mE - `
       |               |
        ` d1 < -------´
        

It goes sour in modules D and E, but if I look at the dependency tree everything looks as expected (e.g. version conflicts are resolved as expected).

One thing I might add is that I systemically use EclipseKeys.withSource := true.
And when I run sbt updateSbtClassifiers, I get a somewhat unexpected failed download:

[warn]  ::::::::::::::::::::::::::::::::::::::::::::::
[warn]  ::              FAILED DOWNLOADS            ::
[warn]  :: ^ see resolution messages for details  ^ ::
[warn]  ::::::::::::::::::::::::::::::::::::::::::::::
[warn]  :: com.typesafe.sbteclipse#sbteclipse-plugin;5.2.4!sbteclipse-plugin.jar(src)
[warn]  ::::::::::::::::::::::::::::::::::::::::::::::

I will note, the latter was observed by trying pretty much anything, without any success.
As stated, everything works, I'd just like to get some understanding why it produces the error and ideally how to avoid it, as seeing errors from "build output" hurts the eyes.

sbt: 1.1.4
sbt-eclipse: 5.2.4
scala: 2.12.5

Start by reproducing the reported multi-module dependency graph with sbt 1.1.4 and sbt-eclipse 5.2.4, then run sbt eclipse and sbt updateSbtClassifiers. Trace how transitive dependencies and EclipseKeys.withSource := true are handled in the Eclipse project generation path; done means the cause is explained and the repeated artifact errors are eliminated or clearly documented.