You hit the nail on the head 
I knew of the existence of folder colors but never even considered that It was a plugin
Indeed, when I disabled Python: folder-color it stopped the error-messsage.
Good to know, because now I have something more solid to put in the bugreport.
As for the second issue, you are right again, it must be some library that is commonly shared between apps. do you have an educated guess which one it could be ?
P.S. Related to the wonky behaviour of caja extensions window you showed,
not only 'caja' but also 'transmission-gtk' is affected.
I suspect more a GTK issue than a python-plugin issue here.
Strangely enough after a recent update, both behaved normally again.
I wonder if it lasts.