When cooking with fenugreek personally, I have found that processing them in a grinder is the best way to use them in a dish. If they are not ground fine enough they can remain a bit more textured. Longer cooking time in liquid can help with the breaking down of the texture as well. However, it is best to just start out with grinding them as fine as you can.
In response to the mustard seeds, I leave them whole, or grind them. Depending on how I plan to use them. They can be prepared in dishes both ways. They too break down in liquid much easier than the fenugreek seeds. So the crunchy texture you mentioned, may have been from the fenugreek, not the mustard seeds. Cooking duration can play a role too, just to keep that in mind.