The nature of Chiss Force Sensitivity is different between the two canons, although they share the idea that the Force is very rare among the Chiss.
In Disney canon, the Chiss know the Force as the "Third Sight". They receive precognitive visions, but evidently don't have or know about any other Force talents. These seers are almost always women. No particular mention is made (that I can see) of their place in society.
In Legends canon, the Chiss see the Force as an impurity and strongly discriminate against it. Force Sensitives are exiled or given medical treatments to suppress their connection to the Force. On the other hand, those who do manifest powers show the full range of Force abilities that we're familiar with in other races. No mention is made of any gender preference.
There are some minor quibbles about the details of their government, but since the Chiss government in Legends is not the most stable body (having at least two, and possibly three, major configurations just during the time of the New Republic) I wouldn't count those as contradictions as such.