This is relatively minor, but I wanted to report it anyway. If you had a script with a comment that is too wide for the current workspace window, the Script workspace will automatically wrap that comment on a new non-numbered line. (I wish it were an option to wrap long lines or not - I personally don't like it, especially for command-steps.) But if you resize the window to fit the width of the Comment line, the blank line it created in order to wrap the comment sometimes doesn't disappear.
There is a workaround: click into the comment so it's being edited, then click out.
See the attached screen shot. The only difference between the two images is that I widened the Workspace window a bit. The first image shows the comment on two lines, the second one shows the vestigial extra-line after the window was widened.
OS X 10.11.6