While the pastor should not have spoken "angrily" to the EMHC, who may have been acting in ignorance, he was indeed correct that the EMHC acted improperly. It would have been better though for the pastor to educate the EMHC in a kind, firm manner than to speak harshly to him.
But for the EMHC to treat consecrated hosts in the same manner that he might carry spare change or a used handkerchief is indeed an abuse of the Eucharist. EMHCs who take the Eucharist to those in the community who cannot come to Mass -- whether they be imprisoned, hospitalized, or homebound -- are supposed to transport the Eucharist as carefully, mindfully, and directly as possible to those to whom they are carrying the Eucharist. That means that this EMHC should have arranged to receive the consecrated hosts from the sacristan just before heading over to the jail for the 2:35 PM service. He should not have carried them around in his suit pocket for six hours.