This is an interesting question. I would say from the point of view of humanity that discrimination exists in all parts of the world. As you know the world is not a perfect place.
In Israel there are many tensions. You can read about these tensions almost everyday in the news. The most common type of discrimination that is pointed out is the discrimination that people from Arab descent feel in Israel. They say that there are biases in common opinion, media, housing, education and many other areas as well. Also it does not help that there are often military conflicts with neighboring Arab nations.
To be sure Israel has strong anti-discrimination laws, but so does the United States. Laws are one thing, personal attitudes are another.
Another groups that has spoken about discrimination are non-white Jews. In particular, Ethiopic Jews has stated in the past that there was discrimination against them due to the color of their skin and their African descent.