Well in Vedas, animal sacrifices are prescribed. But there came a time, when real purposes behind the sacrifices probably got forgotten and people started doing the rituals wrongly and were merely slaughtering animals for their own sake but the excuse was that since it is allowed in scriptures, so nothing wrong.

In order to stop this practice Lord Vishnu incarnated as Buddha. And, since animal sacrifice is Vedic, he had to preach an anti-Vedic doctrine to delude the Jinas who were misusing the prescription of animal sacrifices found in the scriptures.

This reason is mentioned in [Jayadeva Goswami's Dashavatara Stotram][1]:  



> Buddha Avatâra:
> 
> 
> 
> 
> nindasi yajña-vidher ahaha s'ruti-i-jâtam |
> 
> Decrying slaughter according the rules of Vedic sacrifice,
> 
> 
> sadaya-hridaya dars'ita-pas'u-ghâtam |
> 
> 
> You are compassionate of heart with the poor animals.
> 
> kes'ava dhrita-buddha-s'arîra |
> 
> O Kes'ava in the form of Buddha! Hail Hari! Lord of the universe.  
> 
> 
> jaya jagadîs'a hare,  jaya jagadîs'a hare, jaya jagadîs'a hare  ||  
    


So, basically, for this particular incarnation, he came to preach against Vedic doctrines and to stop mass slaughtering innocent animals in the name of Vedic sacrifices.




  [1]: http://bhagavata.org/music/text/dasavatara.html