The most notable change in SF has been the delayed light cycle after pedestrian crosswalk comes on. There was a spike in deaths after that change and I understood why immediately - drivers were timing the light by watching the crosswalk countdown and/or the cross traffic's light cycle. Your light used to turn green just as the other direction's light turned red. When they suddenly changed all the light I noticed a fair number of cars jolt forward then stop, confused, until their light actually changes 4 seconds later.
I'm not sure how this change results in deaths directly, but it definitely added to road rage out there. When the light does change and a car is turning, the expectations are different now. Pedestrians are in the middle of the street already and are less wary of cars jumping out because before there was a moment when everyone would figure out the situation before moving (ideally). Now people are mid-crosswalk and have no idea when the cars' light is going to change which leaves pedestrians more vulnerable.
Another issue I imagine is cars that are making a legal right turn on a red light. The driver looks to see if they can go and have their head turned the exact opposite direction of the crosswalk and wouldn't be aware of when the crosswalk symbol changes. Meanwhile, pedestrians aren't expecting a car to suddenly turn into them 2 seconds after they step into the crosswalk and it is a recipe for disaster. I don't see how they can fix that now without banning all turns on red.
There is also a particularly ugly intersection at Laguna and Geary where they instituted a delayed green when crossing over Geary. People were getting run over in the crosswalks because there is an extra long crosswalk on both sides and cars were turning from both directions with other cars getting backed up and unable to go around them. Because there isn't room for dedicated turn lanes, they have one side go then the other side go, but people lose their shit when they see the southbound cars coming at them for 15 seconds while their light is still red because all prior experience at other lights indicates they should also have a green light when other cars are going... I have seen multiple cars simply drive through that red light and one time 3 cars in a row just decided to go despite the red. They finally put up a sign that says "delayed green" which seems to be helping, but it is an imperfect solution and another counter-intuitive solution.