Are there any specific PHP functions or settings that could cause subqueries to be ignored?

Subqueries may be ignored in PHP if the `PDO::ATTR_EMULATE_PREPARES` setting is enabled. This setting can cause PDO to emulate prepared statements, which may not support subqueries in certain cases. To ensure that subqueries are not ignored, you should disable `PDO::ATTR_EMULATE_PREPARES` and use real prepared statements.

// Disable PDO::ATTR_EMULATE_PREPARES
$pdo->setAttribute(PDO::ATTR_EMULATE_PREPARES, false);

// Use real prepared statements
$stmt = $pdo->prepare("SELECT * FROM table WHERE column = (SELECT other_column FROM other_table)");
$stmt->execute();