diff --git a/src/main/java/org/opentripplanner/routing/algorithm/raptoradapter/transit/mappers/TransfersMapper.java b/src/main/java/org/opentripplanner/routing/algorithm/raptoradapter/transit/mappers/TransfersMapper.java
index 3cb259d3a67..74a5d7a6352 100644
--- a/src/main/java/org/opentripplanner/routing/algorithm/raptoradapter/transit/mappers/TransfersMapper.java
+++ b/src/main/java/org/opentripplanner/routing/algorithm/raptoradapter/transit/mappers/TransfersMapper.java
@@ -19,6 +19,11 @@ static List<List<Transfer>> mapTransfers(StopModel stopModel, TransitModel trans
 
     for (int i = 0; i < stopModel.stopIndexSize(); ++i) {
       var stop = stopModel.stopByIndex(i);
+
+      if (stop == null) {
+        continue;
+      }
+
       ArrayList<Transfer> list = new ArrayList<>();
 
       for (PathTransfer pathTransfer : transitModel.getTransfersByStop(stop)) {
diff --git a/src/main/java/org/opentripplanner/routing/algorithm/raptoradapter/transit/mappers/TransitLayerMapper.java b/src/main/java/org/opentripplanner/routing/algorithm/raptoradapter/transit/mappers/TransitLayerMapper.java
index 210c8b42066..546a97b1d6e 100644
--- a/src/main/java/org/opentripplanner/routing/algorithm/raptoradapter/transit/mappers/TransitLayerMapper.java
+++ b/src/main/java/org/opentripplanner/routing/algorithm/raptoradapter/transit/mappers/TransitLayerMapper.java
@@ -190,12 +190,21 @@ static int[] createStopBoardAlightTransferCosts(
     if (!tuningParams.enableStopTransferPriority()) {
       return null;
     }
+    int defaultCost = RaptorCostConverter.toRaptorCost(
+      tuningParams.stopBoardAlightDuringTransferCost(StopTransferPriority.ALLOWED)
+    );
     int[] stopBoardAlightTransferCosts = new int[stops.stopIndexSize()];
 
     for (int i = 0; i < stops.stopIndexSize(); ++i) {
-      StopTransferPriority priority = stops.stopByIndex(i).getPriority();
-      int domainCost = tuningParams.stopBoardAlightDuringTransferCost(priority);
-      stopBoardAlightTransferCosts[i] = RaptorCostConverter.toRaptorCost(domainCost);
+      // There can be wholes in the stop index, so we need to account for 'null' here.
+      var stop = stops.stopByIndex(i);
+      if (stop == null) {
+        stopBoardAlightTransferCosts[i] = defaultCost;
+      } else {
+        var priority = stop.getPriority();
+        int domainCost = tuningParams.stopBoardAlightDuringTransferCost(priority);
+        stopBoardAlightTransferCosts[i] = RaptorCostConverter.toRaptorCost(domainCost);
+      }
     }
     return stopBoardAlightTransferCosts;
   }
diff --git a/src/main/java/org/opentripplanner/transit/service/StopModel.java b/src/main/java/org/opentripplanner/transit/service/StopModel.java
index 763aa504c40..4f55ca25b5b 100644
--- a/src/main/java/org/opentripplanner/transit/service/StopModel.java
+++ b/src/main/java/org/opentripplanner/transit/service/StopModel.java
@@ -162,6 +162,7 @@ public Collection<GroupStop> listGroupStops() {
     return groupStopById.values();
   }
 
+  @Nullable
   public StopLocation stopByIndex(int stopIndex) {
     return index.stopByIndex(stopIndex);
   }