diff --git a/doc/versionHistory.rst b/doc/versionHistory.rst
index 2e440874..8f20728d 100644
--- a/doc/versionHistory.rst
+++ b/doc/versionHistory.rst
@@ -6,6 +6,14 @@
 Version History
 ##################
 
+.. _lsst.ts.wep-12.4.1:
+
+-------------
+12.4.1
+-------------
+
+* Fixed bug where CalcZernikesTask fails when the number of intra/extra stamps is not equal
+
 .. _lsst.ts.wep-12.4.0:
 
 -------------
diff --git a/python/lsst/ts/wep/task/calcZernikesTask.py b/python/lsst/ts/wep/task/calcZernikesTask.py
index 9c80be27..87eeaeba 100644
--- a/python/lsst/ts/wep/task/calcZernikesTask.py
+++ b/python/lsst/ts/wep/task/calcZernikesTask.py
@@ -238,6 +238,12 @@ def createZkTable(
                 zkCoeffCombined.flags,
             )
         ):
+            # If zk is None, we need to stop. This can happen when running
+            # paired Zernike estimation and the number of intra/extra stamps
+            # is not the same
+            if zk is None:
+                break
+
             row = dict()
             row["label"] = f"pair{i+1}"
             row["used"] = not flag
diff --git a/python/lsst/ts/wep/task/donutStampSelectorTask.py b/python/lsst/ts/wep/task/donutStampSelectorTask.py
index 89bfdea2..341979c4 100644
--- a/python/lsst/ts/wep/task/donutStampSelectorTask.py
+++ b/python/lsst/ts/wep/task/donutStampSelectorTask.py
@@ -172,8 +172,10 @@ def selectStamps(self, donutStamps):
         entropySelect = np.ones(len(donutStamps), dtype="bool")
 
         # Collect the entropy information if available
+        entropyValue = np.full(len(donutStamps), np.nan)
         if "ENTROPY" in list(donutStamps.metadata):
-            entropyValue = np.asarray(donutStamps.metadata.getArray("ENTROPY"))
+            fillVals = np.asarray(donutStamps.metadata.getArray("ENTROPY"))
+            entropyValue[: len(fillVals)] = fillVals
             if self.config.selectWithEntropy:
                 entropySelect = entropyValue < self.config.maxEntropy
         else:
@@ -184,9 +186,10 @@ def selectStamps(self, donutStamps):
         snSelect = np.ones(len(donutStamps), dtype="bool")
 
         # collect the SN information if available
+        snValue = np.full(len(donutStamps), np.nan)
         if "SN" in list(donutStamps.metadata):
-            snValue = np.asarray(donutStamps.metadata.getArray("SN"))
-
+            fillVals = np.asarray(donutStamps.metadata.getArray("SN"))
+            snValue[: len(fillVals)] = fillVals
             if self.config.selectWithSignalToNoise:
                 # Use user defined SN cutoff or the filter-dependent
                 # defaults, depending on useCustomSnLimit
@@ -210,8 +213,10 @@ def selectStamps(self, donutStamps):
         fracBadPixSelect = np.ones(len(donutStamps), dtype="bool")
 
         # collect fraction-of-bad-pixels information if available
+        fracBadPix = np.full(len(donutStamps), np.nan)
         if "FRAC_BAD_PIX" in list(donutStamps.metadata):
-            fracBadPix = np.asarray(donutStamps.metadata.getArray("FRAC_BAD_PIX"))
+            fillVals = np.asarray(donutStamps.metadata.getArray("FRAC_BAD_PIX"))
+            fracBadPix[: len(fillVals)] = fillVals
             if self.config.selectWithFracBadPixels:
                 fracBadPixSelect = fracBadPix <= self.config.maxFracBadPixels
         else:
diff --git a/tests/task/test_calcZernikesTieTaskCwfs.py b/tests/task/test_calcZernikesTieTaskCwfs.py
index 2c46ae82..3005f82b 100644
--- a/tests/task/test_calcZernikesTieTaskCwfs.py
+++ b/tests/task/test_calcZernikesTieTaskCwfs.py
@@ -269,3 +269,15 @@ def testWithAndWithoutPairs(self):
         # Check that the averages are similar
         zkAvgUnpaired = np.mean([zkAvgExtra, zkAvgIntra], axis=0)
         self.assertLess(np.sqrt(np.sum(np.square(zkAvgPairs - zkAvgUnpaired))), 0.30)
+
+    def testUnevenPairs(self):
+        # Test for when you have more of either extra or intra
+        # Load the test data
+        stampsExtra = self.donutStampsExtra
+        stampsIntra = self.donutStampsIntra
+
+        # Increase length of extra list
+        stampsExtra.extend([stampsExtra[0]])
+
+        # Now estimate Zernikes
+        self.task.run(stampsExtra, stampsIntra)