Similar thing happened to me. Could be just random chance, but as Date I had a clan leader die reasonably quickly, his son (a leper) took over and ruled for 30 years without an heir. I had him commit sepuku (experimenting with ordering a vassal who didn't like me to give up his titles had destroyed his honor) so his brother could take over the clan. But then in a period of about 3 years the leper's brother randomly died (age 47) and then HIS son the new heir died (age 20). Each time I got a new court, had to restart project build times, and had reduced vassals. It would be great if they would add the blood drop back to characters so I could see who the hell is in my dynasty.
It was all just so random. "Hey now you're no longer clan leader. Also, this other guy died, so now you're no longer daimyo."
And super frustrating because all the while the ostensible clan leader was letting the Uesugi dig into the Nanbu up north, where I was set for expansion before the chain of death destroyed my family.
Maybe realistic, but good lord...
I dunno how random it is... You ordered your clan leader with no sons and a single brother to commit suicide. Then the brother and his son happened to die in quick succession. That sounds purely like bad planning on your part. Were the brother and nephew married to 4 women each? If not then that might explain your lack of eleigble sons.