in the CC view create project with following structure:
project1
-project1.ipr
-project1.iml
-src
---......
-modules
--module1
----module1.iml
----src
------......
i.e. there is one top-level module 'project1' and one nested module 'module1'. The folder 'modules' that contains the module1's content root is marked as excluded for 'project1' module (if the folder is not marked excluded, the same problems occur)

Enable ClearCase for it specifying single vcs root with directory = project_dir:

--> 1) if the 'modules' directory is not added yet, it is impossible to add it to CC from IDEA (and thus all the files/folders from module1 cannot be added)
2) the activity cannot be defined for the module1 changes, so they always appear in Default cl
3) attempt to rename some folder etc. in the 'module1' module leads to 'cannot start cleartool' errors

If the separate vcs directory is set for module1, everything workd fine