sql_table.cc:

  Fix bug #3749: if there were several indexs that made an automatically generated FOREIGN KEY index redundant, then MySQL miscalculated the number of keys, and the AUTO_INCREMENT flag was forgotten by MySQL from a PRIMARY KEY. There were probably a multitude of other errors caused by this.

sql/sql_table.cc

@@ -683,6 +683,11 @@ int mysql_prepare_table(THD *thd, HA_CREATE_INFO *create_info,
     {
       while ((key2 = key_iterator2++) != key)
       {
+	/*
+        foreign_key_prefix(key, key2) returns 0 if key or key2, or both, is
+	'generated', and a generated key is a prefix of the other key. Then we
+	do not need the generated shorter key.
+        */
         if ((key2->type != Key::FOREIGN_KEY && !foreign_key_prefix(key, key2)))
         {
           /* TO DO: issue warning message */
@@ -693,10 +698,17 @@ int mysql_prepare_table(THD *thd, HA_CREATE_INFO *create_info,
             key->name= ignore_key;
           else
           {
-            /* Remove the previous, generated key */
-            key2->name= ignore_key;
-            key_parts-= key2->columns.elements;
-            (*key_count)--;
+            /*
+	    Remove the previous, generated key if it has not yet been
+	    removed. Note that if we have several identical generated keys,
+            the last one will remain and others get removed here.
+	    */
+            if (key2->name != ignore_key)
+            {
+              key2->name= ignore_key;
+              key_parts-= key2->columns.elements;
+              (*key_count)--;
+            }
           }
           break;
         }