The changed "equals" in 2.12.0 (fix for JAVA-416) calls canonicalize for nested objects, but not for objects in lists.
Example in Scala:

val one = com.mongodb.util.JSON.parse("""{"list": [{"x":1, "y":2}]}""")
val two = com.mongodb.util.JSON.parse("""{"list": [{"y":2, "x":1}]}""")
one == two

Result is false in 2.12.0, true in 2.11.4.