I booked two tickets from online app from Lisbon to Porto and return on 28th Jul, 2018. Lisbon to Porto journey date was 9th Sep, 2018 and return date is 13th September, 2018. We came to Porto on 9th, September 2018. Then I modify the return date to 12th September 2018 on 10th Sep, 2018. It was shown that I have to pay 19.40 euro to modify whereas it deduct 86.40 euro. Basically they take to and from ticket price again for two tickets (43.20 per person). They take the Lisbon to Porto price again and also the full price of Porto to Lisbon whereas the ticket is modifiable. I am not sure what is the problem. Is there anyone who can guide me how shall I get refund.
nsn has a point in the comments: you are paying the full fare now because since the changed return journey is very close, the promo discount doesn't apply anymore.
As described on the relevant page, emphasis theirs:
If you want to have your ticket reissued and get the discount again (limited to the number of special offer seats on each train), the new journey date has to be at least 5, 8 or more days away (including the purchase date and up to a maximum of 60 days in advance) from when it is reissued.
Outside these periods and conditions, the ticket is reissued for a ticket without discount and the difference in prices will be charged.
Note that this doesn't explain why you saw a different number on the site.