Welcome to the forum, Jose.
Unfortunately, when the liner sits on a flat surface, it can't direct water that gets through the mud bed to the drain.
And if the drain flange where the liner attaches is sitting above the level of the floor, you would have a puddle of water until it's deep enough to spill into the drain. Eventually that water will stagnate and cause some odors you won't like.
So far, you're not too deep into this, especially since you're questioning your mud bed anyway. It would be best to take up that mud very carefully without damaging the liner underneath, and start over with a properly built shower.
There's plenty of information available in our liberry under the shower construction threads. I would recommend you spend a little time reading through the ones that apply to your situation. We'll be here to answer any questions you have along the way.