Make sure the mesh is triangulated when exporting it from your 3D app so that the triangulation matches between Toolbag, Substance and other apps. You should rebake your maps in Toolbag after reexporting
Make sure you're baking using the Mikk tangent space in Toolbag
Make sure the Tangent Orientation is matched up between the apps, if you're baking with Right-Handed Tangent Orientation in Toolbag, it should be set to OpenGL in Substance. If Left-Handed, it should be set to DirectX
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A few things to try: