Check with your bank also. Most of times the banks have tie-ups with the retail stores for promoting EMI schemes. Check with your bank, that you were told there will be no extra GST on the EMIs - most likely they will tell that they will give all this back as a cashback after 3 or 6 months (or whenever your EMI ends).
I remember something similar with my purchase of AC from Croma via ICICI. I had to check with ICICI about why they are charging extra stuff like GST.
However, in my case I took EMI scheme because there was additional 1500 Rs off if we engaged EMI scheme.
You mean to say that for a Soundbar of 50000, Reliance agreed for 6000 discount - hence the value becomes 44000. Now you are paying this 44000 as EMIs. However, the invoice value shows 42000?
This is definitely something fishy.