The rooting in such cases is caused due to the higher endogenous auxins. You may try to subculture it on basal medium followed by medium supplemented with any safer cytokinin (which will not challenge culture's genetic fidelity). 

Also, the type of explant you use for culture initiation largely governs this phenomenon, so try some other explants, which are known to have less concentration of auxins in them. It should work. All the best! 

This observation seems to reveal that the plant you are dealing with has high endogenous content of growth substances showing auxin like activity. The way to deal with this kind of situation would be to try some anti auxins like TIBA or maleic hydrazide or phenolics which inhibit auxin like activity

If you are not interested in reducing the concentration of auxin you can add to the culture medium charcoal or polyvinyl pyrrolidone

I did find roots coming out from my leaf explants at certain auxin conc. I took care of the problem by adjusting auxin cytokinin ratio - have a look at my papers on micropropagation and in vitro rooting