Index: src/select.c
==================================================================
--- src/select.c
+++ src/select.c
@@ -5464,18 +5464,23 @@
   SrcList *pTabList,           /* Search for self-joins in this FROM clause */
   struct SrcList_item *pThis   /* Search for prior reference to this subquery */
 ){
   struct SrcList_item *pItem;
   for(pItem = pTabList->a; pItem<pThis; pItem++){
+    Select *pS1;
     if( pItem->pSelect==0 ) continue;
     if( pItem->fg.viaCoroutine ) continue;
     if( pItem->zName==0 ) continue;
     if( sqlite3_stricmp(pItem->zDatabase, pThis->zDatabase)!=0 ) continue;
     if( sqlite3_stricmp(pItem->zName, pThis->zName)!=0 ) continue;
-    if( sqlite3ExprCompare(0, 
-          pThis->pSelect->pWhere, pItem->pSelect->pWhere, -1) 
-    ){
+    pS1 = pItem->pSelect;
+    if( pThis->pSelect->selId!=pS1->selId ){
+      /* The query flattener left two different CTE tables with identical
+      ** names in the same FROM clause. */
+      continue;
+    }
+    if( sqlite3ExprCompare(0, pThis->pSelect->pWhere, pS1->pWhere, -1) ){
       /* The view was modified by some other optimization such as
       ** pushDownWhereTerms() */
       continue;
     }
     return pItem;

Index: test/with1.test
==================================================================
--- test/with1.test
+++ test/with1.test
@@ -1041,7 +1041,26 @@
   WITH c(i)AS(VALUES(9)UNION SELECT~i FROM c)SELECT max(5)>i fROM c;
 } {0}
 do_execsql_test 20.2 {
   WITH c(i)AS(VALUES(5)UNIoN SELECT 0)SELECT min(1)-i fROM c;
 } {1}
+
+# 2018-12-26
+# Two different CTE tables with the same name appear in within a single FROM
+# clause due to the query-flattener optimization.  make sure this does not cause
+# problems.  This problem was discovered by Matt Denton.
+#
+do_execsql_test 21.1 {
+   WITH RECURSIVE t21(a,b) AS (
+    WITH t21(x) AS (VALUES(1))
+    SELECT x, x FROM t21 ORDER BY 1
+  )
+  SELECT * FROM t21 AS tA, t21 AS tB
+} {1 1 1 1}
+do_execsql_test 21.2 {
+  SELECT printf('',
+     EXISTS (WITH RECURSIVE Table0 AS (WITH Table0 AS (SELECT DISTINCT 1)
+                                       SELECT *, * FROM Table0 ORDER BY 1 DESC)
+             SELECT * FROM Table0  NATURAL JOIN  Table0));
+} {{}}
 
 finish_test