The basics are that NCM doesn't return complete search results when there is a large amount of matches to be found. Additional details can be found in this forum post
"NCM search" incomplete results?
This was confirmed with a tech support rep on a desktop sharing session, where we searched for the string "community" and only found matches in a handful of our nodes (~500), while building a rule in Compliance manager found that 2980 nodes of our 3000 in NCM had the word community in them. This was tech support case #677235
So, the suggestion is to fix it so that complete search results are returned, or if its determined that there are too many to return in a web page, offer the choice to download the results. It would probably be nice to be given the option to download the results anyway.