This is an entirely odd observation as far as my understanding goes.
Screen shots to follow.

User Settings:
Members-only collection
Test Users in groups without back-office access, not allowed to post meta comments, only regular comment

What happened:
1) Test User publishes a post
2) Admin adds meta comment
3) Meta comment is visible only to Test User >> all good so far
4) Test User clicks on link to reply to meta comment and writes reply
5) Test User's meta comment is not visible amongst regular comments, but total comment count goes up. Test User cannot see its own meta comment reply.
6) Test User's meta comment is visible amongst regular comments when accessed via menu link widget "Latest Comments". Other test user can see all these comments as well.

Questions:
a) If users are not allowed to post meta comments, why are there links that suggest that they are?
b) Why does the 'reply to meta comment' link actually allow the creation of a comment? (At least the other links tell the user that they cannot post meta comments.)
c) What happened to the meta comment reply? It seems stuck between regular comment and meta comment judging by its visibility in one view but not in another.
d) How can I avoid that this happens in the future?