Sometimes you also need to compare the resulting script to the capture file that was recorded. The .cap file should be a 100% accurate representation of the traffic generated between browser and server - if you're seeing a bunch of "extra" calls in this then this is the traffic you're app is generating and its only right that its in the script.
If on the other hand the capture file has less URLs in it than the script, there may be a legitimate issue and you need to contact Customer Support.
If you're interested in cleaning up the script, you can make these show up as additional sub-requests by using a traffic filter - under options, convert, advanced, traffic filters, create a filter in the bottom listbox that says ".htc"
When you reconvert the script, they'll show up in a more condensed form in the C script, and will disappear from the Visual Navigator script entirely*
Hope that helps!
* - not entirely, they're actually moved to the additional subrequests node for the page they're a part of.