Here's the information MadCap Technical Support provided:
Thank you for contacting MadCap Technical Support, apologies on the delay. The reference to <! [CDATA[]] > is valid code, but please note that I have submitted a Feature Request on your behalf (#79003) with our development team regarding the removal of such insertion. You will be notified via email if this feature becomes available in a future patch or release version.
Below is an explanation of CDATA for reference. Typically these are brought in through an import into Flare.
http://www.w3schools.com/xml/dom_cdatasection.asp
At this time, the scripts would need to allow the inclusion of the CDATA tags. However, if you have nothing in the tags but an empty space, you can execute a Find and Replace for the project and remove them.