There is one example from the book "Greek Fire, Poison Arrows, and Scorpion Bombs" by Adrienne Mayor.

There is a poisonous flower in Asia minor who's nectar does not harm the bees, but produces toxic honey. The locals knew about this, but the Romans did not. The Heptakomites used it to set an ambush for the Romans:

...they gathered up great numbers of wild honeycombs dripping with toxic honey and placed them all along Pompey's route. The Roman soldiers stopped to enjoy the sweets and immediately lost their senses. Reeling and babbling, the men collapsed with vomiting and diarrhea, and lay on the ground unable to move. The Heptakomites easily wiped out about one thousand of Pompey's men.

There are some assertions that the Germans used trained bees on British troop in the Battle of Tanga. The battle was fought in what is modern day Tanzania, and during the course of the fighting on November 4th 1914 several bee hives were disturbed by gunfire, releasing swarms of bees. The British 98th Infantry Regiment was routed by the bee attacks, and the Loyal North Lancashire Regiment was also hit. According to Paul von Lettow-Vorbeck the officer commanding the German forces in their colony in East Africa, the bees attacked the Germans as well, putting out of actions all of the machine-guns in one of the German machine-gun companies, at a moment he describes as "decisive" in his memoirs. So while the bees were not trained, or used on purpose, the intervention of local wild life had a large effect on the battle, contributing to the British defeat.

Sources

Paul Emil von Lettow-Vorbeck, My Reminiscences of East Africa; (London, Hurst, [n.d.]), accessed October 24, 2013, http://archive.org/details/myreminiscenceso00lettuoft.

Edward Paice, Tip and Run (London: Weidenfield and Nicholson, 2007).

In New Zealand we have a toxic native plant called Tutu. It's deadly - miiligrams can kill you. We have to get all honey harvested after 1 January lab tested.