To reproduce this bug, take an account that hasn't been active for say a day, or at least long enough to outlive the session garbage collection and log in with that user.

Next, deactivate that user from the quick tools in the user overview ACP module.

Doing this will call
$user->reset_login_keys($row['user_id']);

Within the reset_login_keys method all session keys for that user are destroyed.

Because of that, the session_gc method which is responsible for updating the last_active field for the user in the users table using the sessions table, never gets a chance to update that last_active date and you lose the true last active time for the user.