What makes Benito Hoover think that there is something wrong with Bernard Marx?
I think what you are referring to is what happens in the elevator car in Chapter 4. Lenina Crowe has talked to Bernard about the two of them going to New Mexico together. When she did Bernard got all embarrassed.
After Lenina leaves, Benito talks to Bernard about how good looking Lenina is and what a good body she has. Remember that in this society people are supposed to think of each other sexually and be promiscuous, so this would not be seen as improper. But Bernard looks unhappy and doesn't even want the Soma that Benito offers.
This makes Benito think something is wrong with him.