diff --git a/lucene/backward-codecs/src/test/org/apache/lucene/backward_index/TestBackwardsCompatibility.java b/lucene/backward-codecs/src/test/org/apache/lucene/backward_index/TestBackwardsCompatibility.java
index 08ab49e94fa..748cd2c527d 100644
--- a/lucene/backward-codecs/src/test/org/apache/lucene/backward_index/TestBackwardsCompatibility.java
+++ b/lucene/backward-codecs/src/test/org/apache/lucene/backward_index/TestBackwardsCompatibility.java
@@ -128,7 +128,6 @@ import org.apache.lucene.util.InfoStream;
 import org.apache.lucene.util.Version;
 import org.junit.AfterClass;
 import org.junit.BeforeClass;
-import org.junit.Ignore;
 
 /*
   Verify we can read previous versions' indexes, do searches
@@ -2245,7 +2244,6 @@ public class TestBackwardsCompatibility extends LuceneTestCase {
   // #12895: test on a carefully crafted 9.8.0 index (from a small contiguous subset
   // of wikibigall unique terms) that shows the read-time exception of
   // IntersectTermsEnum (used by WildcardQuery)
-  @Ignore("re-enable once we merge #12900")
   public void testWildcardQueryExceptions990() throws IOException {
     Path path = createTempDir("12895");
 
diff --git a/lucene/core/src/java/org/apache/lucene/codecs/lucene90/blocktree/IntersectTermsEnum.java b/lucene/core/src/java/org/apache/lucene/codecs/lucene90/blocktree/IntersectTermsEnum.java
index 9475c0de5f8..fb5e0523f10 100644
--- a/lucene/core/src/java/org/apache/lucene/codecs/lucene90/blocktree/IntersectTermsEnum.java
+++ b/lucene/core/src/java/org/apache/lucene/codecs/lucene90/blocktree/IntersectTermsEnum.java
@@ -120,6 +120,8 @@ final class IntersectTermsEnum extends BaseTermsEnum {
     assert setSavedStartTerm(startTerm);
 
     currentFrame = f;
+    outputAccumulator.push(currentFrame.arc.output());
+
     if (startTerm != null) {
       seekToStartTerm(startTerm);
     }
@@ -184,8 +186,7 @@ final class IntersectTermsEnum extends BaseTermsEnum {
     int idx = currentFrame.prefix;
     assert currentFrame.suffix > 0;
 
-    outputAccumulator.reset();
-    outputAccumulator.push(arc.output());
+    int initOutputCount = outputAccumulator.outputCount();
     while (idx < f.prefix) {
       final int target = term.bytes[idx] & 0xff;
       // TODO: we could be more efficient for the next()
@@ -198,9 +199,11 @@ final class IntersectTermsEnum extends BaseTermsEnum {
     }
 
     f.arc = arc;
+    f.outputNum = outputAccumulator.outputCount() - initOutputCount;
     assert arc.isFinal();
     outputAccumulator.push(arc.nextFinalOutput());
     f.load(outputAccumulator);
+    outputAccumulator.pop(arc.nextFinalOutput());
     return f;
   }
 
@@ -343,6 +346,7 @@ final class IntersectTermsEnum extends BaseTermsEnum {
           throw NoMoreTermsException.INSTANCE;
         }
         final long lastFP = currentFrame.fpOrig;
+        outputAccumulator.pop(currentFrame.outputNum);
         currentFrame = stack[currentFrame.ord - 1];
         currentTransition = currentFrame.transition;
         assert currentFrame.lastSubFP == lastFP;
@@ -429,6 +433,7 @@ final class IntersectTermsEnum extends BaseTermsEnum {
               currentFrame = null;
               return null;
             }
+            outputAccumulator.pop(currentFrame.outputNum);
             currentFrame = stack[currentFrame.ord - 1];
             currentTransition = currentFrame.transition;
             isSubBlock = popPushNext();
diff --git a/lucene/core/src/java/org/apache/lucene/codecs/lucene90/blocktree/IntersectTermsEnumFrame.java b/lucene/core/src/java/org/apache/lucene/codecs/lucene90/blocktree/IntersectTermsEnumFrame.java
index 2b0e05a0b09..9f6bb75788e 100644
--- a/lucene/core/src/java/org/apache/lucene/codecs/lucene90/blocktree/IntersectTermsEnumFrame.java
+++ b/lucene/core/src/java/org/apache/lucene/codecs/lucene90/blocktree/IntersectTermsEnumFrame.java
@@ -89,6 +89,8 @@ final class IntersectTermsEnumFrame {
 
   final ByteArrayDataInput bytesReader = new ByteArrayDataInput();
 
+  int outputNum;
+
   int startBytePos;
   int suffix;
 
diff --git a/lucene/core/src/java/org/apache/lucene/codecs/lucene90/blocktree/SegmentTermsEnum.java b/lucene/core/src/java/org/apache/lucene/codecs/lucene90/blocktree/SegmentTermsEnum.java
index 30a4529c5da..f8e3c50bcb2 100644
--- a/lucene/core/src/java/org/apache/lucene/codecs/lucene90/blocktree/SegmentTermsEnum.java
+++ b/lucene/core/src/java/org/apache/lucene/codecs/lucene90/blocktree/SegmentTermsEnum.java
@@ -495,7 +495,7 @@ final class SegmentTermsEnum extends BaseTermsEnum {
       targetUpto = 0;
       outputAccumulator.push(arc.nextFinalOutput());
       currentFrame = pushFrame(arc, 0);
-      outputAccumulator.pop();
+      outputAccumulator.pop(arc.nextFinalOutput());
     }
 
     // if (DEBUG) {
@@ -569,7 +569,7 @@ final class SegmentTermsEnum extends BaseTermsEnum {
           // if (DEBUG) System.out.println("    arc is final!");
           outputAccumulator.push(arc.nextFinalOutput());
           currentFrame = pushFrame(arc, targetUpto);
-          outputAccumulator.pop();
+          outputAccumulator.pop(arc.nextFinalOutput());
           // if (DEBUG) System.out.println("    curFrame.ord=" + currentFrame.ord + " hasTerms=" +
           // currentFrame.hasTerms);
         }
@@ -767,7 +767,7 @@ final class SegmentTermsEnum extends BaseTermsEnum {
       targetUpto = 0;
       outputAccumulator.push(arc.nextFinalOutput());
       currentFrame = pushFrame(arc, 0);
-      outputAccumulator.pop();
+      outputAccumulator.pop(arc.nextFinalOutput());
     }
 
     // if (DEBUG) {
@@ -841,7 +841,7 @@ final class SegmentTermsEnum extends BaseTermsEnum {
           // if (DEBUG) System.out.println("    arc is final!");
           outputAccumulator.push(arc.nextFinalOutput());
           currentFrame = pushFrame(arc, targetUpto);
-          outputAccumulator.pop();
+          outputAccumulator.pop(arc.nextFinalOutput());
           // if (DEBUG) System.out.println("    curFrame.ord=" + currentFrame.ord + " hasTerms=" +
           // currentFrame.hasTerms);
         }
@@ -1187,14 +1187,27 @@ final class SegmentTermsEnum extends BaseTermsEnum {
 
     void push(BytesRef output) {
       if (output != Lucene90BlockTreeTermsReader.NO_OUTPUT) {
+        assert output.length > 0;
         outputs = ArrayUtil.grow(outputs, num + 1);
         outputs[num++] = output;
       }
     }
 
-    void pop() {
-      assert num > 0;
-      num--;
+    void pop(BytesRef output) {
+      if (output != Lucene90BlockTreeTermsReader.NO_OUTPUT) {
+        assert num > 0;
+        assert outputs[num - 1] == output;
+        num--;
+      }
+    }
+
+    void pop(int cnt) {
+      assert num >= cnt;
+      num -= cnt;
+    }
+
+    int outputCount() {
+      return num;
     }
 
     void reset() {