Minecraft Version: 1.21.0
Litematica version: litematica-fabric-1.21.1-0.19.50
Mallilib version: malilib-fabric-1.21.1-0.21.0

Schematic when being overlaped by another schematic

Schematic just on its own

I've tried a new instance of Minecraft with just litematica, mallilib and fabric (defult settings) and had the same result
this happen for me in single player and multiplayer

Overlapping placements are an issue already because of just trying to decide how it's even supposed to work. Obviously two blocks can't be in the same place, so one of the placements has to "win". There is an option in Generic -> placementReplaceBehavior to control whether placements will override blocks already set by previous placements (they are handled according to the loaded placements list order, I believe).