Spice Jet Airlines — missing 500 rs in the total amount I have spent

I have booked chennai to hyderabad flight on 02 nov 2017 and return on 06 nov 2017 in spicejet flight via YATRA. The total fare was Rs. 2988.
And according to spicejet policy for seat booking seperately Rs.200 each up and down i have paid for seat booking. The total fare including seat was for Rs. 3388. Since it is an official trip i was supposed to claim for refund for the total amount of Rs. 3388.
But to my surprise the ticket invoice i have received for up and down including seat booking was coming as Rs. 2888 chennai to hyderabad - Rs. 1220 and hyderabad to chennai - Rs. 1668 which is Rs. 500 less than the amount i have booked.
without seat booking amount of Rs. 400 the ticket rate is coming to Rs. 1468 + Rs. 1020 = Rs. 2488.
There seems to be a disappearance of Rs. 500 which i suppose must have gone as service charge or booking fees.
When enquired with yatra customer care they are pinpointing spicejet for missing money and spicejet also saying that yatra is responsible.
In spite of spending money, I am unable to figure out where it went and I need a valid receipt for this.
My PNR:KDRQHK, NBK8MD
The receipt issued by spicejet is having a shortage of Rs 500 from the money I have spent including seat booking