It's possible to have the tooltip element visible behind the title and content elements when:
This is particularly notable if your jquery-ui widgets have padding.
See https://jsfiddle.net/nktb9n9o/9/ vs https://jsfiddle.net/nktb9n9o/8/ - version 8 has my minor fix included
See stephenriddell/qTip2@3955aef for a very incomplete start to a fix (it works for my use cases, so I've stopped for now, sorry)
Off the top of my head some other cases that need to be handled before this should be considered for merging:
Tooltip padding, not on the side of the tip, eg. top left tip, no top padding exists, but left padding does, and the tip is positioned above the padding, rather than above the interior of the element
Title and content margins causing the tip to be visually next to the tooltip, similar cases - margin may be on the same side as the tip, or it may be on an adjacent side and the tip is near that side.
Similar (but maybe a separate issue) - if the tooltip has a border, but you can't see its background, it would make sense to use that border on the tip instead of the one from the title/content.