Shales are generally non-calcareous, fine grained and finely laminated deep water sediments. The problem with some shales is they have a high organic content, indeed, there are a class of shales called "oil shales" which can be processed to produce oil. There was an shale bed in Southern England which actually caught fire and burnt for years.
That said, oil shales are unusual, and very very few have enough organics to cause trouble in an aquarium. The symptom would be a film on the water surface.
I have used shales in aquaria without trouble.