Well, that’s because he wasn’t doing so out of any good intentions. He was just saying it to sound nice, but, actually, he was just interested and wanted to play with Kurisu. He wasn’t thinking of how Kurisu would feel about this “coming out of the shell” thing and frankly, he just didn’t care at that point in time, as long as he could have his fun. He had no need to be gentle or considerate towards Kurisu and his struggles.
That’s why even when part of Kurisu acknowledged that he had some feelings of affection and desire for Niina, there was also a part of him that’s extremely conflicted and resistant - because he can feel that Niina had always been insincere towards him.
It was only when Kurisu tried to break it off that Niina had some realization of his own feelings towards Kurisu and of how he had been such an asshole all along.
I get that Niina wanted to get Kurisu to come out of his shell and accept that he is gay but it was off putting how forceful he was being in the beginning.