Thank you for sending me your file. I have opened an issue for this bug:
I am not sure what is going wrong, or how this part of Skyline is supposed to work.
It looks like you can work around this error by going into
Settings > Transition Settings > Full Scan > MS/MS Filtering > Isolation Scheme > <Edit Current...>
and then unchecking the box that says "Specify Target".
However, I am not sure what other effects doing that would be.