When making a dummy booking ( in economy ) for the route in question, after selecting the flights, it shows 2 options

Pay With Miles
Pay With Cash

The Pay with miles option shows miles required to be 15000 plus 11273 for the surcharges = 26273 plus $30.50 in tax
The Pay with cash option shows miles required to be 15000 plus $124.00 for the surcharge plus $30.50 in tax

Each of these is per person

It looks like the amount charged is correct.

At the final payment screen , how much payment did it state it was going to take?

Or here's another way. How did your final screen look like when you booked? Was it A or B? and what combination of charges were you expecting to see debited.

A



Or



B



?

The route is IKA-DXB. And this is how the price was disclosed to me:

https://www.dropbox.com/s/hybym9migv9ju9w/1.jpg

Instead of $93.50, I was charged $463.50

if there is a mistake in pricing, has the airline agreed to give you a refund?

EK accepted to cancel the tickets and issue a refund, but cancellation is not an acceptable solution for passengers, because they have made other nonrefundable hotel and tour reservations and need to travel on those dates.
(Furthermore, miles were transferred to EK from Amex and cannot be returned to Amex.)

It sounds like your choice is to pay the $120 per person or cancel

I do not think that you are going to be able to force the airline to accept travel at the desired price

When you got to the credit card payment part and you entered credit card details, how much did it state that you would be charged?

That the miles came from American Express isn't really relevant

Can you transfer the additional miles needed to pay the surcharges in miles and then rebook using miles only?

I did contact them by phone and discussed the issue. First they kept saying $463.50 charge is correct, and nothing else.

At the point where you put the credit card number in, how much did it state would be charged to the card?

In the end, EK is maintaining that the cost is correct ( which doing a dummy booking is supported ) and your choices are to accept it or cancel and rebook in cash on EK or another carrier I think

$93.50

What browser and version were you using? Looks like the function wasn't invoked when the pay with cash radio button was selected.

Chrome Version 39.0.2171.95 m

I don't remember being offered options to select from. So I did not select any radio button to invoke a function.
Perhaps 'Pay with Miles' option was not offered because I didn't have enough miles for that option.

I have just tried with Version 39.0.2171.95 and still gave the surcharges for me

Where does the $93.50 come from?

Maybe I'm missing something, the screen shot you sent shows a cost of $463.50.

The total below the item line shows a cost of $91.50 - is this where the confusion is? Maybe a problem with the webpage, not totalling correctly?

Your booking has 3 people, the examples above done by others show only 1 person.

I tried the route (IKA-DXB) return in saver for 3, the total was 463.50 and there was a column for carrier imposed charges. Hence my question to the OP about the version of browser used. The taxes do add up to 91.50USD so the OP might have mistyped 93.50USD.

I even tried 'forcing' the lower value onto the form (deleting components off the table, modifying the values) but all the calculations are done in the backend and so the displayed figures are not used at all after clicking continue.

I suspect what the OP had was a broken browser at the time of the booking, or EK were doing updates to the website and might have had glitches (but even this is highly unlikely).

The cheapest fare for this route return is just 277.50USD pp. That includes 123USD in base fare, 124USD for surcharges and 30.50USD for taxes.

If you ask me, using 15k miles to save 123 USD is a very bad deal to begin with (and I don't use the word very that often).

That screenshot clearly shows a total of $463.50. The second line is obviously (IMO) a website issue.

I'm guessing you took a screenshot as you noticed the discrepancy?