San Francisco, facing a projected budget deficit of $86 million for the 1988-1989 fiscal year, has paid more than half that amount in overtime since January, according to a city report. City Budget Analyst Harvey Rose's report says San Francisco paid more than $43.5 million in overtime to 63% of its 23,000 employees. The overtime study comes just as the city is considering freezing wages to reduce next year's estimated deficit and the $10-million shortfall projected for the current fiscal year, which ends June 30, 1988. Rose also urged the city to stop paying questionable overtime, come up with a consistent overtime policy for all departments and improve management review of overtime payments. The report found that overtime paid to 14,569 employees from Jan. 1 through Oct. 31 was more than twice the budget of both the district attorney's office and the Department of Public Works.