Moha arose in Arjuna because in the war of Kurukshetra, the opponents are his kinsfolk and kindred, plus, war is about to kill them.
Read following verses of Bhagavad Gita to understand why Arjuna didn't want to fight:
1.28 O Krsna, seeing these relatives and friends who have assembled here with the intention of fighting, my limbs become languid and my mouth becomes completely dry.
1.32-34 O Govinda! What need do we have of a kingdom, or what (need) of enjoyments and livelihood? Those for whom kingdom, enjoyments and pleasures ae desired by us, viz teachers, uncles, fathers-in-law, grandsons, brothers-in-law as also relatives-those very ones stand arrayed for battle risking their lives and wealth.
1.37 Therefore, it is not proper for us to kill the sons of Dhrtarastra who are our own relatives. For, O Madhava, how can we be happy by killing our kinsmen?
[ Quoted from English translation by Swami Gambhirananda ]
So, in the Kurukshetra war, Arjuna feels that it is improper to kill his venerable relatives for the sake of kingdom.
agyatvasa
war was fought between Duryodhana & allies vs Pandavas & allies. It did not involve Drona, Bhisma or Dhritrashtra whom Arjun regarded aspita-tulya
(like father). Also Arjuna primarily fought to defend King Virata who gave them shelter and not for personal gain or loss. Arjuna's disillusionment in Mahabharata was born primarily from the thought of having to kill all the loved ones for material gains. These may be the reasons of Arjuna's different reactions in two different situations.