When would it be appropriate to disagree (in a publication) with a paper you have proofread? I have been asked informally to proofread a paper by a colleague on topic X with an application on Y (constituting about 10% of the paper). After my comments (and those of others), the article was submitted. While it was in review, I looked at Y in more detail for my own work. My own research has led me to believe the conclusions on application Y are quite incorrect.

The paper is now accepted for publication and only typographical edits are accepted, so although I communicated my concerns to my colleague it cannot be included in his paper, even if he wanted to. Would it be wrong for me to prepare a paper on Y myself, disagreeing with my colleague's article (because I had foreknowledge about that article)? If yes, how long should I wait before considering sending something in myself? Naturally, I want to stay on good terms with my colleague.
The fact that you proofread the paper does not change anything: once the paper is published it is available to anyone who wants to criticize it.

The most appropriate course of action however is to try and correct the error in collaboration with your colleague: either by publishing an erratum or a new paper. Or maybe you will decide (after discussion with said colleague) not to correct the error, eg. because it is not important enough. Your colleague will probably not appreciate it if you publish a paper about him being wrong without discussing with him first: doing so is one sure way to destroy any friendship or future collaboration.

Secondly, simply pointing out that another paper is wrong is usually not enough to get a publication.