The NFC champions fought back from 28-6 down against the Baltimore Ravens, but the final four offensive plays cost them the chance to take the lead late in the fourth quarter.
The quarterback told CSN Bay Area: "What most people don't realise is the last few plays weren't the problem. It was the first half.
"We didn't execute in the first half like we should have. So we shouldn't have been in that situation."
The 49ers began their off-season voluntary workouts earlier this week.