"When we got down there the entire story was the whales are late, the whales are late," said Chris Biertuempfel, California's Programs Manager for the Oceanic Society.
Biertuempfel said scientists noticed whales were giving birth outside the San Ignacio Lagoon, the spot they usually go to breed.
"Their journey this year seems to be taking them longer. The fact that they would get down to Baja and give birth outside of the lagoon, shows that they mistimed the migration.," said Biertuempfel, who has several theories of why that may be happening.
He speculates the receding Arctic ice cap may be forcing gray whales to go farther north find food. That means they must travel farther on their migration south to Baja, and if they did not eat enough, they may be simply running out of fatty energy reserves.
That view is shared by Mary Jane Schramm of the NOAA Greater Farallones National Marine Sanctuary.
"Ordinarily we would see this healthy, very linear migration, not really stopping. Going all the way up to the Arctic," said Schramm as she points to a map of the Pacific Ocean to show the typical migration of gray whales once they give birth in Mexico.
Schramm said gray whales don't usually come into the San Francisco Bay. If they do, that means something is wrong.
"It's a desperate move. And it has us alarmed because we've seen this play out before and in 1999 and 2000 when we lost 30 percent of their population," said Schramm.
Thousands of gray whales died in that period. They had recovered, but Schramm fears something similar may be happening again. The culprit could be climate change.
Unlike humpback whales that eat fish along their migration, gray whales are bottom feeders. They eat mudbugs that feed on algae under the Arctic ice to build up their fat reserves and then use that energy for their long migration.
Gray whales have the longest migration of any mammal, between 8,500 to 12,000 miles. They rely on their fat reserves for energy, but if they had to travel farther north for food or did not eat enough for an extended journey, they could starve along the way.
It's as if they are simply running out of gas.
"They are really carefully budgeting their energy, but this trip is longer than they anticipated and so we are starting to see these malnourished individuals," said Biertuempfel.
According to the National Oceanic Atmospheric Administration, 30 whales have turned up dead along the western United States, including two that washed up the same day in Pacifica and Richmond.
Scientists from the Marine Mammal Center and California Academy of Sciences are performing a necropsy on the whales to find out the cause of death.
The Oceanic Society offers gray whale watching trips from Half Moon Bay from January through April and then whale watching trips to the Farallon Islands from May to November.
On every trip, the group has a photographer who will take pictures of the whales so that they can be identified and scientists can map their journey.
The whales are not tagged with GPS devices. Instead, the photographs are run through a program that looks distinguishing features to identify a whale, similar to face recognition technology.
The public can also upload their own whale photos at the website Happy Whale.