On Tuesday, participants received an email stating that a mistake had caused organizers to miscalculate one of the half marathon courses.
Instead of being 13.1 miles, the course through the city was actually only 12.6 miles.
Radhika Bhalla was one of the marathon's participants. She says she figured out something was off while she was running and looking the mile markers.
"It was confusing in the beginning. There's a little bit of like, maybe over time someone made a mistake, the next mile will be longer, we'll make up for it," Bhalla said.
Bhalla says while she just took up running this year, adding that she's come to love the sport. She told our sister station KGO that Sunday's mix-up makes her feel like she's been cheated.
"I got cheated from that experience because I did spend a couple of miles just mentally being like, what's going on, who do I listen to, what pace do I have to follow, do I look at my watch?" said Bhalla.
Similar feelings were shared by Jack Leng. Leng says the weekend's experience has left him with an especially bad impression - not least of all because he says this isn't the first San Francisco Marathon he's done that's had problems.
"To have two bad experiences, I'm like, damn what new mess up are they going to come up with when I do it for a third time?" Leng said.
KGO reached out to marathon officials to get their response on what went wrong.
In a statement, they said, in part:
"We know how disappointed the second-half marathon runners are, and we are as well. Unfortunately, the course route was measured correctly, but the certification map was drawn incorrectly. Mile markers are added based on the map, thus causing the distance calculation error."
Organizers have updated the race times for participants since discovering the mistake.
But for many runners, they think more needs to be done and they're asking for some form of compensation.
"Some people flew in from across the country. This is one of the most expensive races out there, it's like $230 to just register for it. So I think the consternation is definitely justified," said Leng.
In total, around 3,700 people participated in the miscalculated half-marathon.