Of course they do. If the ref adds two minutes and a goalkeeper spends one and a half minute to take a goal kick, do you really not think time should be added on?
Break-up of time added on:
45:00-45:24 - Ball in play
45:59-46:01 - Ball in play
46:31-46:34 - Ball in play
46:57-47:06 - Ball in play
Would you say that the two minutes lost to stoppages has been added back at the end of the period? Out of two minutes, the ball was in play for a grand total of 33 seconds. The ref then had the good taste to wait five seconds, not intend to blow when Maitland-Niles set himself up for the pass, but as soon as Martial broke he put his hand to his mouth to blow up.