A seeming contradicion in meditation

In Buddhism I have often heard the idea that there is nothing wrong with what you are feeling, thinking and sensing, it is only our relation to those things that define/judge them to be bad. Well this has me thinking. If there is such a thing as a "wrong relation" to our thoughts, that relation is itself a thought, which would mean that suddenly there is "something wrong" with our thoughts. So to me this is an apparent contradiction. Either there is something wrong with your thoughts that can be fixed by sitting, or there is not. If there is nothing wrong with your thoughts, feelings, senses, then why sit at all? If there IS something wrong with your thoughts or your relation to your thoughts, that seems to go against the whole non-judgemental awareness idea. In other words, in meditation we say that we are not trying to achieve anything and get anywhere outside the current moment. But getting to that state of mind DOES take effort and training. It IS trying to achieve something. It is moving towards something. It is applying effort in some direction. I can't seem to reconsile these two thoughts. It has been bugging me for a while now, I hope you all can help. Cheers!