How can we embed in CMS without causing conflicts with CSS?

We are attempting to embed Storyline into our intranet. Apparently, when the file is placed on our server, the CMS spiders all folders in that root.  Once the CMS finds something to use, like Javascript and CSS, it auto loads it on the page.

Which means, every page had huge conflicts with the storyline CSS and storyline Javascript. The entire site was affected by the storyline file. Not sure why the CMS would pull it for every page, when it is only needed for that one page.

Does anyone know how to load the storyline file on the server so it doesn’t get spidered and pulled into the entire CMS as a whole?

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