The spatial manipulation perk adds items directly to the player's inventory, bypassing bags and things that listen for item pickup events. Thus if a player has a void satchel to delete cobblestone it isn't deleted, or if the player has a handy bag with pickup enabled the items don't go into the bag, etc. This is kind of inconvenient. I'm not familiar enough with forge to know if simulating pickup events or calling all the listeners with adapted events for the spatial manipulated items is possible.

Another, less annoying issue related to spatial manipulation is that blocks mined by the atomic disassembler from mekanism in vein mode drop normally (except the one actually targetted). Blocks broken by ore excavation, terra shatterer aoe, and thaumcraft destructive are properly teleported. I'm not sure about thaumcraft burrowing.