If you are referring to line 18 in Section C of the CA Adjustments Schedule, "Penalty on early withdrawal of savings," that has nothing to do with your RMD or your 1099-R. It comes from line 18 of Schedule 1 in your federal tax return, which in turn comes from box 2 of a 1099-INT that you entered. The adjustment reduces your federal and California taxable income. It is not a tax penalty. It's a penalty that you paid to the bank that issued the 1099-INT.
(That seems like a rather high penalty. Check and make sure that you entered your 1099-INT forms correctly.)
