There is at least one market I am aware of that covered the event although the contract language seemed to focus on the UK actually leaving the EU (which does not happen immediately) by a certain date rather than the referendum vote itself.
The prediction market below and every fiat prediction market I saw before the referendum vote predicted the "stay" votes were win. Although the polls were close, it appears that both the polls and prediction markets (that predicted the stay votes would prevail) were wrong on the referendum result.
"Long shares will resolve at m฿10 and short shares at m฿0 if the exit of the United Kingdom from the European Union is effective in 2016 or 2017."
Hivemind is the most well known Bitcoin prediction market now in development.
Here are a few more Ethereum DAPPs (which may accept the Bitcoin currency) in various stages of development: