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A few possible solutions:

1. Use a 301 redirect to redirect all traffic from /en to the proper directory as John mentioned.

2. Use robots.txt to block the /en folder. This will keep Google from indexing that folder and hopefully get rid of the duplicate content issues you face.

3. Use Google Webmaster Tools to remove the /en directory from Google all together. This would work best in combination with #2.

Best of luck!