Using Not One of or Does Not Equal excludes the entire record if selected. For example, you are running a constituent query and filtering on Constituency Code not equal to Alumni. Jane Smith has two constituency codes: Parent and Alumni. The query excludes Jane's record from the query because she has the constituency code of Alumni, even though she has another constituency code not excluded from the query.

Instead of using exclusive operators, use inclusive operators, such as 'one of'.

For example, Constituency, Constituency Code one of [all the appropriate constituency codes]).
If the issue still occurs, refer to How to troubleshoot incorrect query results.

NOTE: This rule applies for constituent fields; if running a constituent query but querying on other record types (such as event participations or gifts) the results will include constituents who have one gift/participant which meets the criteria.  In these instances, use a merge query with the Sub operator.