I personally don’t shoot weddings, but edit quite a few over the year. Every company that I work for (wedding or otherwise) has given me a shot list of what should definitely be included in the video. These requests come directly from the client and not the production company that I am working for.
IMO in the future, it would be better if you asked your clients to state what definitely needs to be included in the video. This would avoid a lot of confusion , if a similar situation comes up.
Regarding the payment, that is a personal opinion. If you do send it back with a little memo, you would be their hero. If you don’t, I don’t think it will impact negatively in any way.