Here the wood stacks in backpack before repairs and after three repairs, reducing the duskwood stacks by 1 each and the rowan stack by 54.
I can't quite test the complete cause of this as there are not enough damaged structures present, but it appears that the repair tries to get the best possible match of needed material for the repair, in this case 2 duskwood plus 54 rowan "change".
It would be preferable to just round up the amount needed and take from first stack in inventory, else it keeps deducting from the stash of wood you wanted to save to craft something.