Title just about says it all. This doesn't work for removing floor if there is an object above any part of the flooring.

Does anyone know of a way to fix this? Is the mod dev working on a fix for this? Can someone provide me another solution to the problem?

That is standard vanilla factorio behaviour of the deconstruction planner. I don't have any time to look into it at the moment, and the mod is getting incorporated into vanilla in 0.15. So I'm probably not gonna put much effort into it anymore, with the exception of bugs that come up in the meantime.