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There's nothing jumping out in the logs that's off, it likely is bad information that the client is sending. Most likely it's stemming from the fact that, your package is about 100x as big as a NuGet packages (i.e. .NET libraries) are intended to be. Microsoft will probably never prioritize support for this sort of package, so it's not going to be high on our list either to work-around either.
I would recommend you to find a different way of solving whatever problem you are trying to solve in a different way. If you're packaging applications, you should consider a format actually built for such purposes, like the Universal Package Format or Romp packages.