Bottas was comfortably ahead of Charles Leclerc in the latter stages of the race, before a virtual safety car was called with three laps to go, as a bollard was rolling on the circuit.
Mercedes says that it didn't quite optimise the situation during a very short virtual safety car period, as it prioritised getting Bottas in the right engine modes before anything else.
"This is the shortest VSC we've had so far, 32 seconds total in the duration of which 18 was the VSC deployed to the VSC ending," said chief strategist James Vowles. "That period of time is very, very busy for the drivers.
"First of all, they're towards the pit entry so we have to make sure they know that they're not stopping. That takes a few seconds to get.
"Next, we have to put the power unit into a number of modes to make sure it's safe to operate under a VSC, and ready to go at the restart. From the VSC ending message, it was 14 seconds, a very short period of time.
"During that, Valtteri was in a high-speed corner going into a slow speed corner when the VSC, and went what was called 'unsafe' on his delta time.
"That means that he's negative and if he carries on that way, he could receive a penalty, so priority one was getting him safe relative to the delta time, which took a few seconds to do.
"He did that, he was about four seconds safer to the delta time and everything was good. The problem is when the VSC ended, he didn't have a very long analogue distance to get back into a condition of let's say, zero.
"As a result of it, we lost a few seconds relative to optimum but you would have seen that Charles Leclerc had the same thing, he closed up only by a few tenths.
"He suffered from the same dilemma because he was at the same part of the track as we were. So under the VSC conditions, when it's a little bit longer you have enough time to get back to a delta time of around zero.
"But when it's so short like that, it's just a little bit busy and we didn't quite optimise it fully."
Bottas held on for second to place to take Mercedes' sixth one-two finish of the season, while Bottas took his seventh podium of the year.