Ever since Mako had unlocked the inventory tab, he had used it to store different items inside but he had only ever tested the individual prompts in the inventory tab once and that was when he tested it out for the first when he stored his combat knife inside the system.
The system gave him a single option at that time which was to take it out again as the sell prompt was locked because the shop tab wasn't unlocked yet. Mako quickly understood that the inventory was basically an extra space for him to store and take out things.
Since the system could do the task that Mako commanded it to through his thoughts he never had to physically open the tab again and select the "Take Out" prompt because he could just order the system to directly take something out.
Mako had never tested this with a consumable as he believed it to be the same thing and that he would have to call it out in order to consume it just like everything else.