Why does Will Byers not like girls?

It's not like Will Byers "doesn't like girls" in general. We don't quite know if there is a general aversion to girls or if he is even romantically/sexually attracted to boys instead. That's rather beside the point of these scenes.

Will wasn't directly averted to Max or Eleven. What he didn't like was them "intruding" their original group and "distracting" his friends from their friendship. While the boys are all characterized somewhat as "nerds", we have to understand that Will is pretty much the most vulnerable and shy of the whole group. He basically played the role of the passive victim for about the entirety of the first two seasons (which might even be because of his general vulnerability). He certainly has other worries than girls.

But not only is he lacking a girlfriend "for his own", and thus feels like the 5th wheel of the car in a group of couples (Dustin also got himself a girlfriend, even if she's not present during the season). He also really needs his friends around him, especially after all the stuff that happened to him. He is dependent on the security of his old friends circle and isn't all too comfortable with it getting changed, especially when it seems to him like he's "left alone by the wayisde".

Speaking with a bit of vest-pocket psychology, I would think he generally struggles with growing up (and changing in the course of that), due to all the stress he's experienced. He wants to keep playing D&D with his friends as he did in the good old days, despite them somewhat moving on to more "grown-up" interests.