I believe this is a bug in the crafting of items. If you start crafting something, and leave the menu (backpack, workstation), the item you are crafting won't be guaranteed have its intended number of mod slots, and may come out with less than intended or no mod slots. If you stay in the menu until the item is finished, it should have all its intended mod slots. Also, if you have invested points into faster crafting, and leave the menu while crafting, the time to craft will increase as if you didn't have the perk upgraded. So, until these bugs are fixed, you may want to watch your stuff finish crafting before exiting the backpack/workstation.