Having too much fuel onboard is a weight issue, and when it puts you above legal weights to take off or land you have to remove weight.

In some cases, especially if the overweight is small they will bump some cargo, bags or passengers. Doing that is usually a lot faster than having fuel offloaded, but it may have been a case where those were not reasonable options.

Carrying unneeded fuel weight does cause them to burn more fuel to fly AAA-BBB, just as any weight does. But I very, very much doubt they'd ever offload fuel and cause a delay simply to fly a lighter plane. Decision-makers are incented on on-time performance, and the cost of missed connections and the cost of offload the fuel are both something they want to avoid.