Thanks for the responses. I'm not sure they help very much but I appreciate your time.
Farragut and Nurnberg are fully upgraded except for hull C. Do I really have to get a hull I don't want?
Same with Podvoisky. It is fully upgraded except I did not get the torpedo upgrade. I don't see the point as it adds almost nothing.
There are no branches in those lines, so that is not a factor.
I researched and played the following ships in the tech tree. The only think I can think of is I did not obtain a new captain for some subsequent ships. I don't remember which ones. I used an existing captain. Could that be a factor? If it is, what can I do about it now?