I too have had this problem occurring, as of late. Both with logs (short and long) and grass.
Standing in front of a stack of logs, woodcraft panel open to make small wood blocks for example; pick up a log, put it in the craft window, tools in place, click the button and most of the time everything works as intended....log disappears, blocks show up in inventory, everyone's happy. Randomly however, you click the craft button, the little green action bar pops up and slides to the left like the action is being performed, but when the bar reaches the end, instead of a stack of small wood blocks, you get the message "Materials are missing....." and the log gets removed from the crafting pane but is still on your back. (I've been watching lately and the log does initially move to/show in the crafting pane...right up until the error message when it disappears).
Most of the time I've had my pack open, and a cart with a bin open next to me to move the blocks to. Initially I thought that might possibly be the culprit, but it has also happened when I've just picked up a solo stray log to cut or a bundle of grass to craft and not had a cart.