I was using NEI 2.2.0 and was having items tossed to the ground when I would interact with them inside of the tinkers crafting table while tryting to move them to storage that was connected. I upgraded NEI to 2.2.7 and it still did the same thing. A friend mentioned disabling the bookmark section and sure enough it stopped spitting items onto the ground from the tinker crafting table.

I have a gif of it dropping items and all is fine if I disable bookmarks.