In version 1.20.1-3.2.1 of the Minecraft projection printer mod, there is a bug preventing the automatic placement of Cobblestone Slabs, both when placing them upwards and downwards.

Referenced release: litematica-printer/releases/tag/v3.2.1

Additional details: The automatic placement fails when trying to attach Cobblestone Slabs to another slab or an incomplete block. However, they can be placed correctly when attaching to a full block.

It is not just cobblestone slabs it is all kind of slabs. And the reason is that there is no build in air option. It is hover in 2.5 release. That version has that option and allowed you to place slabs. Hope this helps