Currently using version 0.4.5 and when applying landfill to inland swamp shallow water, the landfill is consumed but the shallow water remains.

After further testing it seems to be working erratically, i restarted the game, and updated some mods, then tried again, this time areas that previously could not be land filled accepted landfill, but still retaining patches that don't accept landfill within them.

I tried disabling inland shallow water, the result is that inland shallow water remains, and now does not even accept an attempt to apply landfill.

I found the problem, a mod called NiceFill was causing the conflict, it attempts to make the landfill look like the nearby chunks....

Have you reported the problem to NiceFill?

Also, disabling inland shallows will stop them from spawning but won't remove existing areas from the game because it is a vanilla tile type.

I didnt report the problem to NiceFill, i will do it now, thanks for your attention.

I'm seeing the same problem but I am not using NiceFill.

You can absolutely landfill all types of water with this mod. If you are having problems with that then you have some other mod that is messing that up, there's nothing I can do about it. Find out which mod is causing the problem and uninstall it or report the problem to that mod author.