Carmen, firstly, please remember that it essential to use idioms exactly as you have learnt them. By exactly, we mean word for word. It is better not to use an idiom at all than to use one inaccurately. Even one word out of place in idiom makes it meaningless. The two idioms you refer to are:
1. To be IN apple pie order.
e.g. His account books were always in apple pie order.
You are right that this means well organised. It's a slightly old-fashioned expression, rarely used by younger people nowadays.
2. To be an apple of discord.
e.g. The question of which grandparents to spend Christmas day with was an apple of discord in the Smith family.
You are mistaken about the meaning of this idiom, which - as you can see from the example above - means a cause for disagreement. As Peter says, this is an image from Greek mythology, and it is very rarely used. In fact, I can't recall a single situation in which I have ever heard anyone use this expression.
As you can see, these idioms aren't opposites. They are completely unrelated.
We can tell from your profile and post that you are an elementary/lower intermediate student of English. Please take our advice and stop worrying about rare idioms. For learners who are still making basic mistakes, the use of half-remembered idioms makes their language look worse, rather than better. At this stage in your studies, it is much more important for you to concentrate on fluent, accurate and natural everyday English.