While picking up the output of cartography_table, the item on the cursor gets consumed.

Steps used in the attachments to reproduce:

• /give @s cartography_table
• /give @s map 2
• /give @s diamond_pickaxe
• Place the cartography_table
• Produce one filled_map
• Open the cartography_table interface and put both filled and empty maps in the inputs.
• With the diamond_pickaxe picked up on your cursor, shift+[left-click] the output of the cartography_table
  The diamond_pickaxe has now been removed from the game.
  You can confirm hasn't been dropped on the ground either by executing /say @e[type=item]