I actually used part of the 400 characters in the feedback after Player Poll #2 describing this issue.

*Stacks not combining automatically without shuffling back and forth with your retainer
*Incomplete stacks located below full ones.

When you start crafting the recipe system pulls from the full stack first- so now you have a stack of 98 and some leftovers, instead of using up the smaller stack first. Did no one notice this in beta?