The plugin only collapses Repeater or Flexible fields that use the Row layout. In its eyes, there's essentially nothing to collapse in the Table layout because the fields occupy a single row.
You'll even notice that a Flexible Field with both row and table layouts will show the collapse button and only collapse the Row fields in use. This is certainly imperfect but the table layout in the plugin makes doing anything else challenging and we haven't figured out a way around that limitation yet.
If this isn't the case, let me know a bit more about how your fields are configured and we'll try to figure out what's going on.