Could 49ers have done more to run down clock?

There was too much time on the clock for the Niners to run it all out, but I do question Shanahan’s play calling when the Niners had a 2nd and 5 twice and proceeded to throw back to back times both times with Garoppolo missing each pass and the Niners going 3 and out both times. I wonder if the Niners ran the ball if they could’ve continued their drive while also running off more clock.