diff --git a/java/ql/experimental/adaptivethreatmodeling/lib/experimental/adaptivethreatmodeling/EndpointCharacteristics.qll b/java/ql/experimental/adaptivethreatmodeling/lib/experimental/adaptivethreatmodeling/EndpointCharacteristics.qll
index 6e383be43ee..9011e64f526 100644
--- a/java/ql/experimental/adaptivethreatmodeling/lib/experimental/adaptivethreatmodeling/EndpointCharacteristics.qll
+++ b/java/ql/experimental/adaptivethreatmodeling/lib/experimental/adaptivethreatmodeling/EndpointCharacteristics.qll
@@ -40,7 +40,7 @@ predicate isKnownSink(DataFlow::Node sink, SinkType sinkType) {
  */
 predicate erroneousEndpoints(
   DataFlow::Node endpoint, EndpointCharacteristic characteristic, EndpointType endpointClass,
-  float confidence, string errorMessage
+  float confidence, string errorMessage, boolean ignoreKnownModelingErrors
 ) {
   // An endpoint's characteristics should not include positive indicators with medium/high confidence for more than one
   // sink/source type.
@@ -63,10 +63,13 @@ predicate erroneousEndpoints(
     not (
       characteristic instanceof IsSanitizerCharacteristic or
       characteristic2 instanceof IsSanitizerCharacteristic
+    ) and
+    (
+      ignoreKnownModelingErrors = true and
+      not knownOverlappingCharacteristics(characteristic, characteristic2)
+      or
+      ignoreKnownModelingErrors = false
     )
-    // and
-    // // We currently know of some sink types that overlap with one another.
-    // not knownOverlappingCharacteristics(characteristic, characteristic2)
   ) and
   errorMessage = "Endpoint has high-confidence positive indicators for multiple classes"
   or
@@ -80,6 +83,7 @@ predicate erroneousEndpoints(
     confidence > characteristic.mediumConfidence() and
     confidence2 > characteristic2.mediumConfidence()
   ) and
+  ignoreKnownModelingErrors = false and
   errorMessage = "Endpoint has high-confidence positive and negative indicators for the same class"
 }
 
@@ -104,6 +108,18 @@ predicate erroneousConfidences(
 //   characteristic1 = ["file creation sink", "other path injection sink"] and
 //   characteristic2 = ["file creation sink", "other path injection sink"]
 // }
+/**
+ * Holds if `characteristic1` and `characteristic2` are among the pairs of currently known positive characteristics that
+ * have some overlap in their results. This indicates a problem with the underlying Java modeling.
+ */
+private predicate knownOverlappingCharacteristics(
+  EndpointCharacteristic characteristic1, EndpointCharacteristic characteristic2
+) {
+  characteristic1 != characteristic2 and
+  characteristic1 = ["mad taint step", "create path"] and
+  characteristic2 = ["mad taint step", "create path"]
+}
+
 predicate isTypeAccess(DataFlow::Node n) { n.asExpr() instanceof TypeAccess }
 
 /**
@@ -374,21 +390,22 @@ private class IsSanitizerCharacteristic extends NotASinkCharacteristic {
   }
 }
 
-// /**
-//  * A negative characteristic that indicates that an endpoint is a MaD taint step. MaD modeled taint steps are global,
-//  * so they are not sinks for any query. Non-MaD taint steps might be specific to a particular query, so we don't
-//  * filter those out.
-//  */
-// private class IsMaDTaintStepCharacteristic extends NotASinkCharacteristic {
-//   IsMaDTaintStepCharacteristic() { this = "mad taint step" }
-//   override predicate appliesToEndpoint(DataFlow::Node n) {
-//     FlowSummaryImpl::Private::Steps::summaryThroughStepValue(n, _, _)
-//     or
-//     // FlowSummaryImpl::Private::Steps::summaryThroughStepTaint(n, _, _) or
-//     // FlowSummaryImpl::Private::Steps::summaryGetterStep(n, _, _, _) or
-//     FlowSummaryImpl::Private::Steps::summarySetterStep(n, _, _, _)
-//   }
-// }
+/**
+ * A negative characteristic that indicates that an endpoint is a MaD taint step. MaD modeled taint steps are global,
+ * so they are not sinks for any query. Non-MaD taint steps might be specific to a particular query, so we don't
+ * filter those out.
+ */
+private class IsMaDTaintStepCharacteristic extends NotASinkCharacteristic {
+  IsMaDTaintStepCharacteristic() { this = "mad taint step" }
+
+  override predicate appliesToEndpoint(DataFlow::Node n) {
+    FlowSummaryImpl::Private::Steps::summaryThroughStepValue(n, _, _) or
+    FlowSummaryImpl::Private::Steps::summaryThroughStepTaint(n, _, _) or
+    FlowSummaryImpl::Private::Steps::summaryGetterStep(n, _, _, _) or
+    FlowSummaryImpl::Private::Steps::summarySetterStep(n, _, _, _)
+  }
+}
+
 /**
  * A negative characteristic that indicates that an endpoint is an argument to a safe external API method.
  *
diff --git a/java/ql/experimental/adaptivethreatmodeling/src/ExtractNegativeExamples.ql b/java/ql/experimental/adaptivethreatmodeling/src/ExtractNegativeExamples.ql
index 0600456b573..9741802db9e 100644
--- a/java/ql/experimental/adaptivethreatmodeling/src/ExtractNegativeExamples.ql
+++ b/java/ql/experimental/adaptivethreatmodeling/src/ExtractNegativeExamples.ql
@@ -35,7 +35,7 @@ where
   characteristic.hasImplications(any(NegativeSinkType negative), true, confidence) and
   // Exclude endpoints that have contradictory endpoint characteristics, because we only want examples we're highly
   // certain about in the prompt.
-  not EndpointCharacteristics::erroneousEndpoints(endpoint, _, _, _, _) and
+  not EndpointCharacteristics::erroneousEndpoints(endpoint, _, _, _, _, false) and
   // Exclude type access nodes because they will never be on a flow path so they're not useful negative examples.
   not EndpointCharacteristics::isTypeAccess(endpoint) and
   // It's valid for a node to satisfy the logic for both `isSink` and `isSanitizer`, but in that case it will be
diff --git a/java/ql/experimental/adaptivethreatmodeling/src/ExtractPositiveExamples.ql b/java/ql/experimental/adaptivethreatmodeling/src/ExtractPositiveExamples.ql
index d69774cf60d..cc833e5d012 100644
--- a/java/ql/experimental/adaptivethreatmodeling/src/ExtractPositiveExamples.ql
+++ b/java/ql/experimental/adaptivethreatmodeling/src/ExtractPositiveExamples.ql
@@ -22,9 +22,9 @@ private import experimental.adaptivethreatmodeling.ATMConfigs // To import the c
 
 from DataFlow::Node sink, SinkType sinkType, string message
 where
-  // If there are _any_ erroneous endpoints, return nothing. This will prevent us from accidentally running this query
-  // when there's a codex-generated data extension file in `java/ql/lib/ext`.
-  not EndpointCharacteristics::erroneousEndpoints(_, _, _, _, _) and
+  // Exclude endpoints that have contradictory endpoint characteristics, because we only want examples we're highly
+  // certain about in the prompt.
+  not EndpointCharacteristics::erroneousEndpoints(sink, _, _, _, _, false) and
   // Extract positive examples of sinks belonging to the existing ATM query configurations.
   (
     EndpointCharacteristics::isKnownSink(sink, sinkType) and
@@ -35,9 +35,16 @@ where
     // Include only sinks that are arguments to an external API call, because these are the sinks we are most interested
     // in.
     sink instanceof ExternalAPIs::ExternalApiDataNode and
-    message =
-      sinkType + "\n" +
-        // Extract the needed metadata for this endpoint.
-        any(string metadata | EndpointCharacteristics::hasMetadata(sink, metadata))
+    // If there are _any_ erroneous endpoints, return an error message for all rows. This will prevent us from
+    // accidentally running this query when there's a codex-generated data extension file in `java/ql/lib/ext`.
+    if not EndpointCharacteristics::erroneousEndpoints(_, _, _, _, _, true)
+    then
+      message =
+        sinkType + "\n" +
+          // Extract the needed metadata for this endpoint.
+          any(string metadata | EndpointCharacteristics::hasMetadata(sink, metadata))
+    else
+      message =
+        "Error: There are erroneous endpoints! Please check whether there's a codex-generated data extension file in `java/ql/lib/ext`."
   )
 select sink, message