Is $5,800 to replace a flat roof a fair price?

I hired a roofer to replace my flat roof and install a sun tunnel. I paid $5800 for the roof and an additional $1400 for a 14-inch sun tunnel, which was confirmed on the paperwork. However, the workers installed a 10-inch sun tunnel, claiming only 10.5-inch joist spacing, and used a cap designed for a pitched roof, not a flat roof. I confirmed with Velux that a curbed 14-inch product is required for flat roofs. The foreman initially tried to justify the pitched cap. I'm standing firm on getting the correct product. I'm meeting with the project manager and foreman to discuss. I'm concerned about a big hole and patch on a brand new roof if they fix it. I haven't paid the second half of the work yet. I'm open to fully removing the sun tunnel and patching the roof, as the light isn't great anyway. I also specifically told them I planned to put deck tiles and furniture on the roof, but the material they used is not walkout-able. It seems no permits were pulled for the work. I'm frustrated because I explained exactly what I wanted and feel like I went 0/2.