theThe same just happened to me today. I tried different browsers from my PC, but on a one-stop route I could only select a seat for free on just one airplane. It seemed like I could not select anything but an 18€ seat on the other airplane, nor an option to skip that step, in spite of their disclaimer:
Seat reservation You can reserve a seat even after you have bought your ticket. You can do so up to the end of the check-in procedure before departure online or via our call centre. There is a fee per seat reservation (depending on the fare bracket) per passenger and leg (on domestic German flights add VAT). If you do not reserve a seat, you will automatically be allocated one at no extra cost when you check in.
Anyway, I tried to check-in from my mobile and even though I could only select "larger seats" again, it did not show any price attached to that. Basically I got a larger seat at no cost.
Hope this helps!