One of the most frequently encountered problems with establishing explants (especially woody perennials) in culture is the production of exudates by the explants.
These exudates are usually considered to be various phenolic compounds that oxidize to form a brown material in the medium.
Pretreatment with an antioxidant (citric or ascorbic acid) can minimize this problem as can frequent transfers to a new medium or adding activated charcoal to the medium.