The behavior the original poster is complaining about is a normal feature of the EFC and has nothing to do with cousin marriages.
When the EFT encounters extended family for a spouse of someone in the selected person's tree, a second record for that spouse is created in a completely separate "island" in the report. The two records are correlated by use of an index number in the upper left corner of each "box". The person locator helps find people who are in more than one place in this report - which can become quite long and complicated very quickly as a file grows.
The single most important strategy in minimizing the number of "islands" and multiple instances of a single person in the report, is to have the "selected", or "base" person be at the bottom of their resepective family - and not an ancestor.
See my examples given in a separate post to see how that works.