When creating Pencil comments in Acrobat or Reader while the tool is selected it will only create a single comment, with all of the drawings as a part of it. If you want to "ungroup" those lines into individual comments, this is the tool for you!  It's free and can be downloaded from here.

You can select to either ungroup all of the Pencil markups in the entire file, or just those that are currently selected. Here's an example. I've drawn a bunch of lines on a blank page.
As can be seen in the Comments List panel, there's only one comment, which contains all of the lines:

I run the tool to ungroup them (see the new menu buttons under Tools):

And the results are that each line is now its own comment and can be selected separately:

For more information about this script, you can contact me directly, and if you find this tool useful and would like to donate, it's always appreciated!