there's no standard for calculating tangent space (mikkt space is hopefully getting there, thank god) so pretty much every 3d software is different. if you bake a normal map in one and import the asset into another (say, from a 3d modeling program to a game engine), your normals may just be a little off or have big fat problems. here's an example of this problem, which i experienced recently. a door model with normals baked in blender; viewed in blender and then in unity.
i ended up fixing it by getting a unity tangent space plugin for xnormal and baking with that. but that's what handplane fixes too.