Very similar thing happened to me in r100.
I could reproduce it like 3 times with blank projects, but when I wanted to reproduce it again to post it here step by step it didn't ocurr anymore.
Was something like:
1. Open new project in folder
2. Add a Sprite
3. Run the project
4. Save as a folder project but in another folder, not the selected in step 1.
5. Close Construct.
6. Open Construct.
7. Open project previously saved in step 4.
8. Run project.
--> Error with the Sprite plugin... Something like "Sprite missing" (I forgot to take a screenshot one of the three times, sorry). I went to the "Animations" folder and there was no sprite, so, for that reason was the error.
Maybe there is a bug with the "Save as folder", and is just difficult to reproduce it several times.
The first time it happened to me was when I was backing up one of my projects and tried to run it. For that reason I tried to reproduce it and I could do it like 3 times with blank projects.
BTW, I don't have any third party plugins installed.