The Briton's gap to teammate Bottas in P1 grew at the end of the VSC, which was deployed when Pierre retired from the race on lap 40.
Hamilton initially suggested that his own mistake had cost him the time, but Mercedes has since confirmed that a number of factors made the five-time world champion lose sight of his delta at the restart.
"During the VSC at the end of the race, you will have seen Lewis lose a couple of seconds of race time relative to Valtteri, which could have been crucial for the win,” said strategy chief James Vowles.
“When the VSC ends, the driver gets a notification on his dash, and that’s something that we have the ability to control what’s displayed and what’s not.
“We asked Lewis to do a number of switch changes, which is normal, to put the car into a more performant mode. But with every change, he lost sight of what that delta time was.
“The other factor that was contributing here was that if you are in a straight line and the VSC ends, all you have to do is manage the throttle, get on the throttle and go straight.
“But Lewis wasn’t, he was in a braking zone for the VSC, one of the most difficult situations because now it’s very difficult to modulate where you are on the delta time and get ready for the VSC restart.
“A combination of all of that put together means that Lewis didn’t make a mistake. It’s where he was on track and a number of switch changes that just masked where he was in exact delta time and he lost around two seconds.”
Vowles added that the Silver Arrows will make improvements to the dash ahead of the Spanish Grand Prix in order to rule out a similar situation in the future.
"We from our side can certainly do more work to make that better in terms of a dash display going forwards to Barcelona, and we will do,” he said.
“The luck of the draw as to where you are under the VSC, unfortunately, will always be the same way.”
Bahrain International Circuit - Winter testing