When trying to use the filler in water it will automatically fill in an additional layer below the area marked off by landmarks no matter if you mark off a 2d area (3 landmarks) or an XYZ 3d area (4 landmarks).

There's no ownership taken on this one, I'm closing it for now. You can carry on discussing on http://mod-buildcraft.com/forums/index.php?board=2.0.

Thanks for opening this issue.
This also happens if you use the "Box" pattern, the layer that is inside water gets doubled.

Greetings, SnowD

In some cases this also happens mid air. I saw this with slabs that I placed as a roof.

I defined a X_1_Z area for the filler and set it to fill this area with slabs. Some of the slabs were placed below the defined area. I could not recognize a pattern for that issue.

Filler + EnderIO as energy source + Glass slabs from Pam's mods.