Depends on what kind of story you're writing with special attention to the fact that your MC lacks confidence and is not a decisive badass.
If the harem members are like party members in a fantasy world then maybe the MC is aware of their feelings, but the MC may be trying to downplay the emotional tension or postpone a decision for the greater purpose of party cooperation and cohesion.
If the harem members are like girls at his high school or a more regular life then focusing on the MCs reasons for not being decisive might be the best option.
Give this MC some internal monologue and backstory. Perhaps he is the understanding and compassionate type.
"My childhood friend A has feelings for me. She doesn't fully realize it herself. Despite her abusive comments, she is afraid of losing me, it's common jealousy, but I can't resolve myself to reciprocate her feelings. Ever since I fucked up that one time and person B got hurt, I couldn't look at her properly anymore. I couldn't trust myself to protect her."
"Girl C, I know she doesn't see the real me, but my heart is always hoping for someone to accept me. I admire her, I really do, her cheerful personality, the confidence that I don't have, the liveliness that eludes me. It makes me wonder if I'm even living compared to someone like her. She's like that and I'm drawn to her radiant smile. It's like a moth to the flame, and even worse is that I know I'm hurting the others around me by clinging to her. I can hear their unspoken words, that I am not someone who deserves to be near her."
I just gave out some general feelings for example. However, the construction of the harem is just as important as the MC and their feelings because relationships involve 2+ people. With a harem, it's not just a relationship between two people, it's a web of interconnected circumstances and feelings. You might do well to set up the girls backstories to explain why they are fighting or stuck courting the same man. Why do the girls tolerate each other? What unofficial and unspoken truces have they signed? Or, why are they trying to rip each others' throats out?
The headache induced by the relationship web, the struggles that the MC has to deal with understanding the circumstances, the MC's actions, that's all good story material!