I'm not sure what your problem is. CFINCLUDES can be nested both on the same
page and in sub pages; however, it can get pesky if the overall HTML gets lost
or if a cfinclude - includes a page with itself included.

For example,

page1.cfm
<cfinclude template="page2.cfm">

Page2.cfm
<cfinclude template="page1.cfm>

This would create an infinite loop (page1 would call page2 and page2 would
call page1 and it would never end.

Also, if you begin a page with the proper header tags and then in the body
include another page with its own header tags, all kinds of bizzare results
happen.

So, you need to ensure that each included file fits approriately within the
structure as if one page were created.

Create a test page and copy the actual code from the page instead of the
cfinclude and see if the overall HTML sructure is still intact (no duplicate
header tags, broken body tags, table tags broken etc.)

Beyond that, I'm not sure how to help.