Yellow spots on fall red raspberry
My raspberries have yellow spots on them and the berry is smaller than they should be. The plants grow six or seven feet tall even after I pruned them to three feet in the spring.
Yellow spots on fall red raspberries sounds like fall rust or late leaf rust.
Penn State has a good page on this disease and a link to some controls
It sounds like you have a fall bearing raspberry. All the fruit you are getting in the fall are from the primocanes which grew this year. The canes you are cutting back to 3 feet have already borne fruit and usually only have a small summer crop unless you are getting a good summer crop you can cut all the canes down at the beginning of the season and only harvest the fall crop. This does make pruning and disease control easier. If you like your summer crop you can continue to double crop.