Kerbal Space Program

Steps to reproduce:

1. Add two control points to your craft, maybe separated by a decoupler.
2. Give your craft a name with the craft name field at the top.
3. Right-click a control point and select Configure Vessel Naming.
4. Decrease priority (or increase, or leave it the same, it doesn't matter) and choose a new name.
5. Observe that the name of the craft changed to the new name.

When configuring vessel names this can get very annoying quick since it can be hard to spot, and once you start saving it saves into a new file. If you then load the original any new changes will be gone, but if your changes aren't immediately obvious, you may not notice, and continue working on your craft. Then, later, you find that you now have two crafts and basically you have to do half the work again.

I would suggest that vessel renaming doesn't affect craft file renaming at all, so that you can change the name of your craft without having to change the name of your save file. It's probably also the easiest fix.

Note: I have Breaking Ground, but that probably doesn't matter.