It's one of two things. The timer itself isn't shutting off when it's supposed to or there's something wrong with the valve. The odds are it's the valve. You could disconnect the wire from the timer to see if the valve shuts off. If not then it's the valve. Does the valve stay shut off once you turn the main back on? I can name 10 reasons off the top of my head why a valve wont shut off. Many similar but specifically different reasons. If you could give me the make and model of valve it would help a lot. Or make and style. Meaning inline valve or anti-syphon valve or valve adapter.
If I can't fix it, it's broken!