The fill and replace tools in BL only work on one type of tile at a time, it doesn't work on multiple tiles at the same time.
I.E. if you have a giant pocket of air tiles, you can fill that in, but if you have a pattern of repeating 2x2 tiles, you can't just fill that with a different set of 2x2 tiles with a single click of the fill tool, it works exactly as a fill tool in a paint program would. The replace tool just replaces all instance of one tile with another and that's it.
I have had zero issues with these two tools and use them in my mods so I assume there's some sort of misunderstanding on how they work.