Some people are under the illusion that what is intended by this statement is that it is impermissible to repudiate (others) regarding any affair in which difference of opinion is held. So based upon this (illusion of theirs), it becomes impermissible to disapprove of a Munkar (an evil) unless there is complete agreement in doing so. This is a wrong understanding which necessitates the termination of enjoining good and forbidding evil.
The scholars (i.e. of Ahlus Sunnah) hold differences of opinion in most of the Masaa’il (i.e. the verdicts on fiqh and subsidiary issues). And what is correct regarding this statement ‘Laa Inkaar Fee Masaa’il Al-Khilaaf- There should be no repudiation in affairs of Khilaaf (differing)’ is that there should neither be harshness in (one’s) disapproval nor (in one’s) criticism regarding those issues about which there is no manifest proof to be taken as the final (verdict). And the basis upon which this is founded is that the issues of khilaaf (differing) are of two categories:
The First Category: They are those issues of khilaaf in which there is proof necessitating that it should be taken as the final (verdict). So here, the proof must be taken and the other statement (or opinion) in opposition is discarded. And whoever follows the statement (or opinion) that is established to be in opposition to the proofs, then he is to be repudiated.
The Second Category: It is those issues of khilaaf in which the proof has not been manifested in order to be taken as the final (verdict). It is an affair in which the evidences contend with each other or the views are at variance. This is an issue of Ijtihaad, and there is neither disapproval nor reprimand against the one in opposition; rather advice is given to acquaint (each other) with the statement that carries more weight. This second category of (khilaaf) is what is intended by the statement ‘Laa Inkaar Fee Masaa-il Al-Khilaaf’ which some people have understood in an unrestricted manner. 
Shaikh Rabee Bin Haadee Al Madkhalee (hafidha-hullaah) said:
We do not say that there are people of ijtihaad amongst ahlul bidah because they are followers of desires, and Allaah and His Messenger have testified to this. The misguided innovator stirs up discord (or splitting) and errs, and then says to you, ‘This is ijtihaad’.
When Hikmatiyaar and the misguided parties (in Afghanistan) murdered Shaikh Jameel Ur-Rahmaan, they said: ‘This is ijtihaad’. Making lawful the spilling of the blood of the Salafis is Ijtihaad to them. This is what it is! They (ahlul bidah) do not fall into an affair of misguidance or a calamity except that they say, ‘This is ijtihaad’. This is diluting Islaam. It is falsehood, misguidance and bidah mixed with truth when the mistakes of the (true and qualified scholars of ijtihaad)- for which they are rewarded- are placed at the same level with innovation about which the Messenger (sallal-laahu-alayhi-wasallam) said that it will be in the fire. 
 [Source: Ibaaraat Moohimah, page 25’ by Shaikh Muhammad Bin Umar Saalim Baazmool (may Allaah preserve him). Abridged and slightly paraphrased]
 Ajwibatul Allaamatush Shaikh Rabee Bin Haadee Al Madkhalee Alaa As-ilah Abee Rawaaha Al-Manhajiyyah; page: 20