Had Mourinho's hand not got tied up by the 2 unfortunate and unexpected injuries, he could have probably brought on Baker later in the game. OR had Torres, Willian not squandered chances to kill the game off completely, Baker could have come on. At 2-0, the game was not completely safe with Swindon creating some decent chances and that's probably why he didn't want to bring Baker on and besides, Mourinho probably felt more important then given the circumstances to give Ba game time to improve his match fitness and match sharpness so that it will benefit the first team in the long run this season.