I admit that I haven't checked your site yet,
but the most popular mistake is when webmasters use template module position (that exist in layout) and the same module is used in SPPB in module addon. Then Joomla thinks that module should be displayed twice.  That's why we recommend using, for example, sppagebuilder module postion if module should be published only in SPPB page(s) or SPPB module(s). 
Yes, 2nd popular mistake is when custom CSS make mess, and is used to hide modules (objects), and used CSS rules are not fully correct, sometimes small mistake make a big difference.  
For advanced module settings I always recommend using AMM from Regular Labs, but it's advanced tool, not for everyone. 
Remember that Joomla is like robot but without AI, it only does what you will command.  Of course, J! sometimes has mood swings, but that's a topic for another article.