There could be multiple reasons.
The search result count you see on LinkedIn includes profiles without names. In other words the profiles without any names aka " LinkedIn member" are included in the count. Whereas We-Connect only pulls profiles with real names and skips unnamed profiles.
If you are using keywords or a lot of filters in your Sales Navigator search, please save the search and then copy-paste the saved search URL in we-connect. Such a custom search URL contains a lot of parameters in the URL string that it can break during copy-paste. We recommend saving the search on Sales Navigator and use the saved search URL, which contains just one parameter and provides accurate results. Please read this article if you need help on how to save a search in sales navigator.
You may be doing 2nd & 3rd connection search but have checked the 1st connection check box accidentally. Please see this article.
You may have included 1st connections in your LinkedIn or Sales Navigator search when you are actually looking for 2nd and 3rd connections. It is best to select 2 & 3rd connections directly in LinkedIn.
With Sales Navigator, you can save a max of 2500 contacts per search. With a free Linkedin account, you can save up to 1000 contacts per search. If you have more than the above contacts in our search, please narrow your search using Linkedin or Sales Navigator search filters.
If you manage multiple accounts, please make sure that you are not using a sales navigator search URL on an account that does not have a sales navigator account.