Fix: The subquery adds a prefix for the table alias.

system/Database/BaseBuilder.php

@@ -577,7 +577,7 @@ public function fromSubquery(BaseBuilder $from, string $alias): self
     {
         $table = $this->buildSubquery($from, true, $alias);
 
-        $this->trackAliases($table);
+        $this->db->addTableAlias($alias);
         $this->QBFrom[] = $table;
 
         return $this;
@@ -2952,7 +2952,7 @@ protected function buildSubquery($builder, bool $wrapped = false, string $alias
             throw new DatabaseException('The subquery cannot be the same object as the main query object.');
         }
 
-        $subquery = strtr($builder->getCompiledSelect(), "\n", ' ');
+        $subquery = strtr($builder->getCompiledSelect(false), "\n", ' ');
 
         if ($wrapped) {
             $subquery = '(' . $subquery . ')';

system/Database/BaseConnection.php

@@ -882,7 +882,12 @@ public function table($tableName)
      */
     public function newQuery(): BaseBuilder
     {
-        return $this->table(',')->from([], true);
+        // save table aliases
+        $tempAliases         = $this->aliasedTables;
+        $builder             = $this->table(',')->from([], true);
+        $this->aliasedTables = $tempAliases;
+
+        return $builder;
     }
 
     /**

tests/system/Database/Builder/PrefixTest.php

@@ -11,6 +11,7 @@
 
 namespace CodeIgniter\Database\Builder;
 
+use CodeIgniter\Database\BaseBuilder;
 use CodeIgniter\Test\CIUnitTestCase;
 use CodeIgniter\Test\Mock\MockConnection;
 
@@ -49,4 +50,40 @@ public function testPrefixesSetOnTableNamesWithWhereClause()
         $this->assertSame($expectedSQL, str_replace("\n", ' ', $builder->getCompiledSelect()));
         $this->assertSame($expectedBinds, $builder->getBinds());
     }
+
+    public function testPrefixWithSubquery(): void
+    {
+        $expected = <<<'NOWDOC'
+            SELECT "u"."id", "u"."name", (SELECT 1 FROM "ci_users" "sub" WHERE "sub"."id" = "u"."id") "one"
+            FROM "ci_users" "u"
+            WHERE "u"."id" = 1
+            NOWDOC;
+
+        $subquery = $this->db->table('users sub')
+            ->select('1', false)
+            ->where('sub.id = u.id');
+
+        $builder = $this->db->table('users u')
+            ->select('u.id, u.name')
+            ->selectSubquery($subquery, 'one')
+            ->where('u.id', 1);
+
+        $this->assertSame($expected, $builder->getCompiledSelect());
+    }
+
+    public function testPrefixWithNewQuery(): void
+    {
+        $expectedSQL = <<<'NOWDOC'
+            SELECT "users_1"."id", "name"
+            FROM (SELECT "u"."id", "u"."name" FROM "ci_users" "u") "users_1"
+            WHERE "users_1"."id" > 10
+            NOWDOC;
+
+        $subquery = (new BaseBuilder('users u', $this->db))->select('u.id, u.name');
+        $builder  = $this->db->newQuery()->fromSubquery($subquery, 'users_1')
+            ->select('users_1.id, name')
+            ->where('users_1.id > ', 10);
+
+        $this->assertSame($expectedSQL, $builder->getCompiledSelect());
+    }
 }

user_guide_src/source/changelogs/v4.2.5.rst

@@ -32,5 +32,6 @@ none.
 
 Bugs Fixed
 **********
+- When using subqueries in the main query, prefixes are added to the table alias.
 
 See the repo's `CHANGELOG.md <https://github.com/codeigniter4/CodeIgniter4/blob/develop/CHANGELOG.md>`_ for a complete list of bugs fixed.