Why comments replies are not showing as indented? Why are comment replies not indented? I have already enabled comments threading in the settings for the content type.

All comments and their replies are shown in the same sequence and it is getting hard to find out to which comment another comment is replying.

I am using the Bootstrap theme. When I change the enabled them to the Bartik theme, comments are correctly shown as expected.
What you can do is to give the "reply" (it might have a unique id or class), some margin left to indent it under the comments.

The reason that it is indented in Bartik, is that Bartik is the standard theme and is fully compatible with drupal core.