Active Directory limits the number of results that can be returned in a single query, this is defined by the MaxPageSize settings in the LDAP Query Policy, the default value is 1000.  If the results of a query exceeds this limit, the server will return a Size limit was exceeded (0x4) error.  To overcome this limit you need to use the Paged Server Side Control, which will return the results over a number of responses, with the total number of results per response not exceeding the MaxPageSize value.  NetTools has the Paged Control is enabled by default and will automatically reconstruct the results into a single output.

The MaxPageSize value is defined in Default Query Policy stored in the configuration partition.

CN=Default Query Policy,CN=Query-Policies,CN=Directory Service,CN=Windows NT,CN=Services,CN=Configuration,DC=x

Attribute - lDAPAdminLimits

You can also define a separate Query Policy at the domain controller and AD site levels, these can be viewed using the Site Browser option.