Having cruft in your top layer is fine and healthy; a sign of a living, evolving system that is still learning how best to do its job and hasn’t prematurely ossified.

The problems occur when a still-crufty layer becomes set in stone, ensuring its base defects go on to pollute everything built on top. That may happen either because its designers lack perspective and cannot accept their precious design is flawed; or because everyone else starts building on top before it is ready for prime-time, then reject all attempts to straighten it out because that would require them to rewrite as well.