Since it is happening only this year I think its some kind of deficit or fungal problem, no need to trow away the tree u just have to find out what the problem is. I also have a potted nagami and it ripened its fruit fine, I have never encountered such problem before, but I only got interested in citrus this summer so dont have alot of experience.....
By the way I dont know if this Is relevant to citrus ,but with tomatoes fruit end blackening is caused by calcium deficiency and too much watering.