for future reference most timers have a small switch that changes the operation from timer to always on. on my timers the switch is not even marked, you have to try it both ways to see which is auto.
you are probably better off having done what you did than say having an hour or two of light in the middle of a dark cycle. i think the only problem you'll have is how long it takes to finish flowering.
I went on vacation and bought brand new timers specifically for this trip. Anyhow they did not ever turn my lights off. The strain is cheese. They are about half way through flowering 5 weeks 12/12. Is there anything I can do or are they all going to herm out?