The City of San Jose's website has a phone number and email address to report concerns about traffic signal timing.  I just called about an issue I have noticed at the intersection of Fruitdale Avenue and Meridian Avenue, and spoke with a very helpful man who told me the traffic signal coordination plan had recently been updated and the City is still fine tuning, and he would write up a work order to look into my concern.   If you have a question about traffic signal timing at an intersection in San Jose, you can contact the City at:
To report non-emergency concerns:
Their website is http://www.sanjoseca.gov/index.aspx?NID=278