There aren't any records specific to Mission Bay but there are three (2 confirmed) in the San Diego area:
The shark attack that killed David Martin in 2008 at Solana Beach, 14 miles northwest of San Diego, may have been the first shark attack in San Diego County in 50 years.
Michelle von Emster was killed in 1994, possibly while swimming off Point Loma, San Diego. The San Diego County medical examiner's office ruled that she was killed in a shark attack; however, some in the law enforcement community have questioned this conclusion and feel that she may have been murdered and dumped in the Pacific Ocean. Her leg was bitten off by a great white shark.
In 1959, Robert Pamperin was free-diving for abalone at Alligator Head, La Jolla Cove. His dive buddy Lehrer heard Pamperin screaming for help, his thrashing body momentarily upright and waist-high out of the water before submerging. Lehrer dove and spotted a 20–23-foot shark thrashing Pamperin in its mouth. The attack was witnessed by several people onshore. An extensive search by police divers and the Coast Guard failed to recover Pamperin's body; only a single swim fin was found. He was seen being swallowed whole, feet-first.