urgh! who would you hold responsible for this fee

So we got a new roof. City permit fees were included. We wanted a solatube installed too. The roofer said his business neighbor does solatube and they use them for install. So we got it.

We had a city permit for the roof. When inspector came, they saw the solatube and denied passing our roof inspection since the solatube was not permitted. Roof company said solartube guy would have to go pull that permit. Solatube company said the roofer should have pulled it when he got the permit for the roof. Roofer offered to go pull it after the fact but the city denied him since he wasn't the installer. Solatube company tells me they don't pull permits so I have to personally do it.

I just spent FOUR f'in hours in the city permit office trying to get the permit. There was major issues and they were horrific to deal with. After the third hour I was so angry and said to the manager "no wonder people never get permits in our city". It pissed him off so much that he added $40 to my permit. I asked why he raised the price and he smiled (in a assy type of way) and said "I added a fine for obtaining your permit after the fact". So all in all, I paid $125. $85 for the permit and 40 for the fine.

I didn't feel like I should be responsible for any of those fees. I purposely hired top of the line installers who have city licensing. I called the roofer first and explained the situation and told them that between them or the solatube installers, I feel they should cover my $125 fees, since I was not told about this. Neither want to pay a penny, but the solatube company said they may pay part of it just to get my returned business (I planned to get two more in the future).

Now I'm wondering if I was irrational since I was so angry. Should I expect one of them to cover all the fees?