I've built a small test to reproduce the bug, which you can see here.

What I think is happening:

• The base template includes the fragment using a path prefix with the folder that contains it (i.e. included/)
• The prefixed path is not valid when used from the leaf template, where the correct path prefix would be ../included/
• The leaf template is resolving the includes in the base template as if the base template belonged to the same folder of the leaf template, which isn't the case

I don't have a fix (yet), but putting this up here for visibility in case others bump into it.