This has been happening to me at least since 0.124 - when I click a line number, both that lind and following one are selected. I assumed that this was a problem in the Select Line package, because I didn’t think the functionality was even there in the core editor. But disabling/uninstalling that package (and also the HightLight Line package) made no difference, so I do suspect faulty functionality in the core editor.
Did you try running Atom in Safe Mode too, just in case?
Just did – problem gone. So it is some package or other… thanks for reminding me!