Yes, I always have that issue. Not sure why it is never fixed. Last trip, I ended up doing the on-line check-in, then I called and told them my issue and they added it there. Actually the first CM I spoke to said they could not do it if I already completed the on-line check-in, so I called back and someone else did it very easily.
Another website issue: I just tried to make a payment and it said "can not process credit card", and then it asked me to enter another credit card. I know my card is fine. Then I checked my credit card and the payment is pending so I went back to the Disney website and it deducted my payment from my balance, even though it indicated that it did not at first.
Sadly, the whole website is still very unreliable. It does make me worry about making ADRs for an upcoming trip on-line.