The issue is possibly down to technical limitations of their webserver/database server setup. Database queries are sometimes done with an automatic restriction on numbers to prevent crashes or memory problems on the servers, and similar issues my arise with the user interface used - Adobe flash. The first questions I always need to know when working a new system with database storage is 'how many records might be involved ?', and 'how are any search results to be handled'. It can be unsafe to allow an unrestricted search.
If this type of numbers issue arises from a search the usual practice would be to either display a warning message on the search result, or to cancel the search and request more details from the user. The National Archives Census searches uses the latter tactic, although sometimes it can be fooled.
The search algorithm also seem to be a little flawed on the site in its current version, as it can give different results depending on exactly how you carry out the search. When I was on to Familysearch about the recent placename problems they said they were planning an update to the site for later this year (I think 'late summer' was mentioned). This upgrade/fix was also due to include searches by registration district.
Shane