www.wysiwygwebbuilder.com

On publish WB it automatically adds
<link href="programs.css" rel="stylesheet">

the project includes the page programs.php.

When the page dioikhtikos28.php is published, it has:
<link href="programs.css" rel="stylesheet">
<link href="dioikitikos28.css" rel="stylesheet">
resulting in the programs.css of the regular page being disrupted.
Which setting do I need to change in the program?

Each page has two CSS files: one for global styles shared across the site, and another for local styles specific to that page.

You can control this via Tools -> Options -> HTML