Rents in San Francisco reached new highs last month. The median for a one-bedroom apartment on the rental platform Zumper hit $3,720 in June. One reason, a new report suggests, is zoning. According to a paper to be published Thursday by the Brookings Institution and the University of California, Berkeley’s Terner Center for Housing Innovation, the most expensive cities tend to have stricter limits on development. Cities that restrict the height of buildings and the number of units per acre, for example, add fewer apartments. And that pushes rents even higher.