Did you bond the mud to the slab with thinset or a slurry of pure portland cement? It sounds like you didn't and the mud is just floating over the slab. It probably shrunk a little, allowing some movement that you are hearing.
Haven't used Mercrete Hydroguard as a liner. I don't have anything negative to say about it, but I do urge you to carefully review their instructions and follow them to the letter. Also, purchase and use a wet film thickness gage to verify you are applying the correct amount of liquid. You are the only QC inspector on your job, and this is the most critical thing you will be doing.
Despite what I said earlier about following the instructions, If they do not include any reinforcing fabric at the corners and the drain connection, please use it anyway. The weak link in this type of shower constuction is where two surfaces are spanned by the membrane. The extra time and money will make for better sleep.
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