That might be something you want to post there: github.com/Scirra/Construct-3-bugs/issues
Especially if you can reproduce it. Generally, a c3p file is just a zip so you can extract it and edit the files with a texteditor, find the duplicate animation name and change it. It might not be that simple though, so beware and backup your project.
In terms of backup, did you setup construct to do automatic backups? If not, I can just recommend that (aswell as doing backups on your own)