diff --git a/lib/cypress/expected_results_calculator.rb b/lib/cypress/expected_results_calculator.rb
index aca98b60..1971e537 100644
--- a/lib/cypress/expected_results_calculator.rb
+++ b/lib/cypress/expected_results_calculator.rb
@@ -52,7 +52,7 @@ def aggregate_results_for_measures(measures, individual_results = nil)
         # If individual_results are provided, use the results for the measure being aggregated
         measure_individual_results = individual_results.select { |res| res['measure_id'] == measure.id.to_s } if individual_results
         # If individual_results are provided, use them.  Otherwise, look them up in the database by measure id and correlation_id
-        measure_individual_results ||= CQM::IndividualResult.where('measure_id' => measure._id, correlation_id: @correlation_id)
+        measure_individual_results ||= CQM::IndividualResult.where('measure_id' => measure._id, correlation_id: @correlation_id, 'extendedData.manual_exclusion': {'$in': [nil, false]})
 
         aggregate_results_for_measure(measure, measure_individual_results)
       end
@@ -62,7 +62,7 @@ def aggregate_results_for_measures(measures, individual_results = nil)
     def aggregate_results_for_measure(measure, individual_results = nil)
       # If individual_results are provided, use them.  Otherwise, look them up in the database by measure id and correlation_id
       begin
-      individual_results ||= CQM::IndividualResult.where('measure_id' => measure._id, correlation_id: @correlation_id)
+      individual_results ||= CQM::IndividualResult.where('measure_id' => measure._id, correlation_id: @correlation_id, 'extendedData.manual_exclusion': {'$in': [nil, false]})
       rescue Exception => e
         Delayed::Worker.logger.info(e.message)
         Delayed::Worker.logger.info(e.backtrace.inspect)
@@ -172,7 +172,7 @@ def create_query_cache_object(result, measure)
         if population_set.stratifications.length > 0
           population_set.stratifications.each do |stratification|
             sub_id = stratification.stratification_id
-            qco = result[measure.hqmf_id]
+            qco = result[measure.hqmf_id].clone
             qco_saved = nil
             qco['result'] = {}
             if qco[sub_id].present?
@@ -196,7 +196,7 @@ def create_query_cache_object(result, measure)
         # if there are only multiple populations but not stratifications
         else 
         sub_id = population_set.population_set_id
-        qco = result[measure.hqmf_id]
+        qco = result[measure.hqmf_id].clone
         qco_saved = nil
         qco['result'] = {}
           if qco[sub_id].present?
@@ -222,7 +222,7 @@ def create_query_cache_object(result, measure)
       elsif measure.population_sets.length == 1 && measure.population_sets[0].stratifications.length > 0
         measure.population_sets[0].stratifications.each do |stratification|
         sub_id = stratification.stratification_id
-        qco = result[measure.hqmf_id]
+        qco = result[measure.hqmf_id].clone
         qco_saved = nil
         qco['result'] = {}
           if qco[sub_id].present?