Relative includes of sub templates/sub snippets don't work, if you use a main.ftl located in a different location/module.
The relative include is the executed on the new location (relative to the new main.ftl).
We had the same problem with all Section templates and removed the relative pathes from the Section templates.
The the singleton paragraph templates still contain these relative includes, see print screen.

Best would be to check all template definitions (and all ftl's for include of macros) if there are still any relative includes left.

All includes, no matter where, should be absolute paths.