diff --git a/components/s3/src/main/kotlin/org/veupathdb/vdi/lib/s3/datasets/DatasetManager.kt b/components/s3/src/main/kotlin/org/veupathdb/vdi/lib/s3/datasets/DatasetManager.kt
index 9846db0b..adae56dc 100644
--- a/components/s3/src/main/kotlin/org/veupathdb/vdi/lib/s3/datasets/DatasetManager.kt
+++ b/components/s3/src/main/kotlin/org/veupathdb/vdi/lib/s3/datasets/DatasetManager.kt
@@ -162,7 +162,13 @@ class DatasetManager(private val s3Bucket: S3Bucket) {
             // Stream is exhausted, construct a dataset out of remaining objects.
             val idsFromObject = datasetIdFromS3Object(stagedObjects.first())
             val pathFactory = S3DatasetPathFactory(idsFromObject.first, idsFromObject.second)
-            this.currentDataset = EagerlyLoadedDatasetDirectory(stagedObjects, idsFromObject.first, idsFromObject.second, pathFactory)
+            try {
+              this.currentDataset = EagerlyLoadedDatasetDirectory(stagedObjects, idsFromObject.first, idsFromObject.second, pathFactory)
+            } catch (e: MalformedDatasetException) {
+              Metrics.malformedDatasetFound.inc()
+              log.warn("Found a malformed dataset with ID $idsFromObject.")
+              return null
+            }
             stagedObjects = emptyList()
             return currentDataset
           }
diff --git a/modules/reconciler/src/main/kotlin/org/veupathdb/vdi/lib/reconciler/ReconcilerInstance.kt b/modules/reconciler/src/main/kotlin/org/veupathdb/vdi/lib/reconciler/ReconcilerInstance.kt
index d2fcb5d4..8127911c 100644
--- a/modules/reconciler/src/main/kotlin/org/veupathdb/vdi/lib/reconciler/ReconcilerInstance.kt
+++ b/modules/reconciler/src/main/kotlin/org/veupathdb/vdi/lib/reconciler/ReconcilerInstance.kt
@@ -72,10 +72,12 @@ class ReconcilerInstance(
 
           // Delete datasets until and advance target iterator until streams are aligned.
           while (nextTargetDataset != null && comparableS3Id.compareTo(comparableTargetId, true) > 0) {
-            logger().info("Attempting to delete dataset with owner ${sourceDatasetDir.ownerID} and ID ${sourceDatasetDir.datasetID} " +
-                    "because ${nextTargetDataset!!.syncControlRecord.datasetID} is lexigraphically greater than our ID.")
+
+            logger().info("Attempting to delete dataset with owner $comparableTargetId " +
+                    "because $comparableS3Id is lexigraphically greater than $comparableTargetId.")
             tryDeleteDataset(targetDB, nextTargetDataset!!.type, nextTargetDataset!!.syncControlRecord.datasetID)
             nextTargetDataset = if (targetIterator.hasNext()) targetIterator.next() else null
+            comparableTargetId = nextTargetDataset!!.getComparableID()
           }
         }