Please help us help you and fill where relevant:
Your LimeSurvey version: Version 3.14.8
Own server or LimeSurvey hosting: hosting
Survey theme/template: customised from fruitty
==================
There are some situation where I get a pop-up window with a warning on it. For example, when not all questions are answered. However, the pop-up window does not disappear after the close button is clicked. It seems to happen when I specifically use this theme.
My expectation: the pop-up window disappears when the close button is clicked.

My guess is that you have introduced a JavaScript error. Try it with an unmodified core theme.

Your LimeSurvey version: Version 3.14.8
Own server or LimeSurvey hosting: hosting

And I am pretty sure that the official Limesurvey hosting by Limesurvey GmbH does not run any instances on Version 3.14.8 anymore.

LS 3.14.8-180829 was released on 29.08.2018, so almost exactly 5 years ago. This sound rather like a "own server" and most probably of a university...