Is it legal in the state of California for a manger to tell you to clock in later.?

Yes, this is legal. A company can dictate when a worker's shift is to start, unless doing so violates the terms of an employment contract or union agreement. Therefore, as long as the employee was not working off the clock, no law has been broken. However, if the employee must remain on the premises and cannot use their time as they see fit while waiting, then such time is compensable and they must be pad for it. So, for example, if the employee was told to wait to clock in but to remain on the premises, then they should have been paid. If, however, they were told to leave the work premises and come back about later and clock in, then such time need not be paid.  

They can't have the employee work off the clock for a half hour: that would be illegal, and an hourly employee is entitled to be paid for all time worked (and could bring a legal action, or complaint to the department of labor for, the unpaid time).
However, employers (e.g. the managers) control when employees may work. A manager can tell an employee to not start working, or even to go home entirely, even if the employee's normal shift had already started. Unless your shift is set out in a written employment contract, so the time you work is contratually enforceable, your employer, through its managers, can adjust the time you may work at will.