According to the documentation array element containment is translated like this:

.Where(c => c.SomeArray.Contains(3))

to

WHERE 3 = ANY("c"."SomeArray")

As I understand this filter cannot use GIN index created on the array column.
So what about changing the translation to:

WHERE "c"."SomeArray" @> ARRAY[3]

or

WHERE "c"."SomeArray" @> '{3}'

There is a difference with NULL element handling though.