Thank you for looking into this issue!
I can reproduce the warning with the following steps:
1. Have the default settings, i.e. "Enable ghost warnings: On"
2. Hold any ghost item (make sure you don't have the actual item in your inventory. For example by selecting a new item in the crafting menu with Q)
3. Place ghost in the sandbox
Result: A warning will be displayed "Missing <item name>"
FWIW, this quick hack would fix the problem:
control.lua L80:
-- ignore blueprint sandbox
if player.gui.left["bpsb-toggle-gui"].visible then return end