diff --git a/metricsaggregator/src/main/java/io/dockstore/metricsaggregator/MetricsAggregatorS3Client.java b/metricsaggregator/src/main/java/io/dockstore/metricsaggregator/MetricsAggregatorS3Client.java
index f6abef3b..b2c2b2fd 100644
--- a/metricsaggregator/src/main/java/io/dockstore/metricsaggregator/MetricsAggregatorS3Client.java
+++ b/metricsaggregator/src/main/java/io/dockstore/metricsaggregator/MetricsAggregatorS3Client.java
@@ -40,6 +40,7 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Queue;
+import java.util.UUID;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import software.amazon.awssdk.services.s3.S3Client;
@@ -146,30 +147,47 @@ private ExecutionsRequestBody getExecutions(String toolId, String versionName, S
         for (MetricsData metricsData : metricsDataList) {
             String fileContent = metricsDataS3Client.getMetricsDataFileContent(metricsData.toolId(), metricsData.toolVersionName(),
                     metricsData.platform(), metricsData.fileName());
-            ExecutionsRequestBody executionsFromOneSubmission = GSON.fromJson(fileContent, ExecutionsRequestBody.class);
+
+            ExecutionsRequestBody executionsFromOneSubmission;
+            try {
+                executionsFromOneSubmission = GSON.fromJson(fileContent, ExecutionsRequestBody.class);
+            } catch (JsonSyntaxException e) {
+                LOG.error("Could not read execution(s) from S3 key {}, ignoring file", metricsData.s3Key());
+                continue;
+            }
+
+            // For each execution, put it in a map so that there are no executions with duplicate execution IDs.
+            // The latest execution put in the map is the newest one based on the principal that S3 lists objects in alphabetical order,
+            // which is returned in an ordered list via getMetricsData.
+            // Note: executions that were submitted to S3 prior to the existence of execution IDs don't have an execution ID.
+            // For the purposes of aggregation, generate one so that the execution is considered unique.
             executionsFromOneSubmission.getRunExecutions().forEach(workflowExecution -> {
-                executionIdToWorkflowExecutionMap.put(workflowExecution.getExecutionId(), workflowExecution);
-                executionIdToValidationExecutionMap.remove(workflowExecution.getExecutionId());
-                executionIdToTaskExecutionsMap.remove(workflowExecution.getExecutionId());
-                executionIdToAggregatedExecutionMap.remove(workflowExecution.getExecutionId());
+                final String executionId = generateExecutionIdIfNull(workflowExecution.getExecutionId());
+                executionIdToWorkflowExecutionMap.put(executionId, workflowExecution);
+                executionIdToValidationExecutionMap.remove(executionId);
+                executionIdToTaskExecutionsMap.remove(executionId);
+                executionIdToAggregatedExecutionMap.remove(executionId);
             });
             executionsFromOneSubmission.getTaskExecutions().forEach(taskExecutions -> {
-                executionIdToTaskExecutionsMap.put(taskExecutions.getExecutionId(), taskExecutions);
-                executionIdToWorkflowExecutionMap.remove(taskExecutions.getExecutionId());
-                executionIdToValidationExecutionMap.remove(taskExecutions.getExecutionId());
-                executionIdToAggregatedExecutionMap.remove(taskExecutions.getExecutionId());
+                final String executionId = generateExecutionIdIfNull(taskExecutions.getExecutionId());
+                executionIdToTaskExecutionsMap.put(executionId, taskExecutions);
+                executionIdToWorkflowExecutionMap.remove(executionId);
+                executionIdToValidationExecutionMap.remove(executionId);
+                executionIdToAggregatedExecutionMap.remove(executionId);
             });
             executionsFromOneSubmission.getValidationExecutions().forEach(validationExecution -> {
-                executionIdToValidationExecutionMap.put(validationExecution.getExecutionId(), validationExecution);
-                executionIdToWorkflowExecutionMap.remove(validationExecution.getExecutionId());
-                executionIdToTaskExecutionsMap.remove(validationExecution.getExecutionId());
-                executionIdToAggregatedExecutionMap.remove(validationExecution.getExecutionId());
+                final String executionId = generateExecutionIdIfNull(validationExecution.getExecutionId());
+                executionIdToValidationExecutionMap.put(executionId, validationExecution);
+                executionIdToWorkflowExecutionMap.remove(executionId);
+                executionIdToTaskExecutionsMap.remove(executionId);
+                executionIdToAggregatedExecutionMap.remove(executionId);
             });
             executionsFromOneSubmission.getAggregatedExecutions().forEach(aggregatedExecution -> {
-                executionIdToAggregatedExecutionMap.put(aggregatedExecution.getExecutionId(), aggregatedExecution);
-                executionIdToWorkflowExecutionMap.remove(aggregatedExecution.getExecutionId());
-                executionIdToTaskExecutionsMap.remove(aggregatedExecution.getExecutionId());
-                executionIdToValidationExecutionMap.remove(aggregatedExecution.getExecutionId());
+                final String executionId = generateExecutionIdIfNull(aggregatedExecution.getExecutionId());
+                executionIdToAggregatedExecutionMap.put(executionId, aggregatedExecution);
+                executionIdToWorkflowExecutionMap.remove(executionId);
+                executionIdToTaskExecutionsMap.remove(executionId);
+                executionIdToValidationExecutionMap.remove(executionId);
             });
         }
 
@@ -180,6 +198,20 @@ private ExecutionsRequestBody getExecutions(String toolId, String versionName, S
                 .aggregatedExecutions(executionIdToAggregatedExecutionMap.values().stream().toList());
     }
 
+    /**
+     * If the execution ID is null, generate a random one for the purposes of aggregation.
+     * Executions that were submitted to S3 prior to the existence of execution IDs don't have an execution ID,
+     * thus for the purposes of aggregation, generate one.
+     * @param executionId
+     * @return
+     */
+    private String generateExecutionIdIfNull(String executionId) {
+        if (executionId == null) {
+            return UUID.randomUUID().toString();
+        }
+        return executionId;
+    }
+
     /**
      * Returns a unique list of directories containing metrics files.
      * For example, suppose the local-dockstore-metrics-data bucket looks like the following.