Where did you read that?
As you are using a commercial theme I have no access to its code, so I cannot inspect the code to see how it is conflicting with Alligator Popup. I would suggest you contact your theme vendor to ask how to deactivate whatever built-in popup feature in the theme is interfering with the plugin.
My best guess for a workaround for this is to hack the Alligator Popup plugin to change the class used to trigger the popup, but be aware that any changes made will be overwritten on the next plugin update unless you rename the plugin to prevent it being updated.
To do this, substitute the word ‘popup’ with a unique class name in:
line 69 of alligator-popup.php:
return '<a href="' . esc_attr($url) . '" class="popup" data-width="' . esc_attr($width) . '" data-height="' . esc_attr($height) . '">' . $content . '</a>';
& line 3 of js/popup.js:
$('.popup').click(function() {