There is no direct night train from Bern to Amsterdam. You must change in Basel. I guess that you are trying to make the reservation through the Interrail/Eurail website? There are better ways to make the reservations than that website. 

What typ of reservation do you want? Seat/couchette/bed?

When are you travelling? There are no direct nighttrains Bern-Amsterdam. You'll need to switch at Basel.

Best book directly via Nightjet or ÖBB. 

Just book it like you would book an ordinary ticket, but you'll need to add in your passenger information that you travel with Interrail. Via the discounts. This is found at the passenger details. You need to Add the Eurail/ Interrail Global pass option as a discount. Et voila, proceed and it should show reservation prices with Interrail discount should show.

Exact step to step guide is found here 

Hi, yes you are right, the basel-amsterdam one. Can you suggest me on which other sites is better searching for? I would book seat but not available on interrail site, so I booked couchette at the moment. 

https://www.nightjet.com/en/#/home

Like I said before, don't forget to put Interrail as a discount at the passenger details. I checked for next month, and seats didn't seem available indeed

The seating carriages do run with an other train number (60402 instead of 402). The shop will show two trains at exactly the same time, so choose the right one.

Book here: https://shop.oebbtickets.at/en/ticket

It will cost 3 €. 

If you'd like to book a seat, don't put "interrail" as a discount. That's wrong and that's why there are no seats available.

Choose "seat reservation only".

Thank you all for your help guys!