My personal guess is more an agent who ignored it - AF seems to have 'standard' contingency plans for the numerous times the web doesn't work properly. I have never been made to pay when I have needed to book over the phone either a paid or an award ticket because the website was wholly or partly down (which has, sadly, happened quite a few times!). I can only imagine that that particular agent either didn't know he could or didn't want to waive the fee and I think cupart is certainly right to request a refund. And as you say, AF might throw a few miles on top of it too.