Home office blunder: Cancelled my valid skilled worker visa because a previous dependant visa application got approved.

Hi seeking advice from anyone who has had a similar experience.

My situation is that I made two visa applications to the home office.

Application1: I made a PBS dependant visa application with my wife in May 2022.
Application2: Due to some issues I decided to apply for a separate skilled worker visa sponsored by my new company in July 2022. On this new application I clearly mentioned that I have a previous pending application with the home office.

I received positive outcome of the application2 in Aug 2022. I believed that the previous application (application1) must have been automatically cancelled, as per the rules.

However, very recently I received a BRP for application1 in my mailbox. So what happened is that application1 was delayed for processing and was approved later on. Now I have a dependant visa instead of the skilled worker visa.

The problem is that I don't want the dependant visa from my wife as we have decided to separate.

How should I approach the home office to re-instate my skilled worker visa? This is clearly an error from them as application1 should have been automatically cancelled/withdrawn, as I made a new application (application2).

My ILR is pending this year and I don't want anything to affect it due to home office blunders.
Kindly advice.