Yunior's nausea is supposedly caused by something associated with the van. The prevailing theory is that it is the upholstery. However, his nausea might be psychological. And this might have something to do with his uncertainty about his identity and his subsequent loneliness.
Yunior's two main older male role models are his brother Rafa and his father (Papi). Both are domineering and use cruelty and threats to control others. But Yunior is more sensitive and therefore more like his mother, his aunt, and his sister. So, he has some difficulties identifying with the male role models in his life and is probably confused that he relates more to his mother. Yunior is also troubled by his father's affair with the Puerto Rican woman. Yunior is anxious around girls whereas his brother is confident to the point of arrogance. At the end of the party, Yunior is a literal and figurative outcast, sitting in the hallway.
Yunior can not articulate what is bothering him when his mother asks. He relates more to her but can not talk to her. But he does attempt to reach out to others in fairly overt ways. He writes an essay for school titled "My Father the Torturer." The teacher makes him write a new essay. He adds "She thought I was kidding." This underscores his loneliness. Even when he articulates his feelings, he is ignored.