Described the bug here:
https://bitbucket.org/Soaryn/xycraft/issue/164/fabricator-advanced-wooden-pipe

Do not know who needs to fix it, but it really needs to be fixed.

the advanced wooden pipe doesn't use ISided, but pulls from everything available. XYCraft declares its "virtual" items to be real items available via the standard IInventory interface. ; hence this is a bug with XYCraft.

This will cause the noted dupe bug with every block in any mod that doesn't use forge ISided.

This specific instance would be a bug with Xycraft. However, adv. wooden pipes should respect ISidedness. (keeping this issue open as enhancement)