It seems to be some kind of bug in PyCharm.
As a workaround, you may remove duplicated entries manually. They are located in config file in PyCharm preferences directory. Default path is ~/.PyCharmxy/config/options/jdk.table.xml, where xy represents version (e.g. PyCharm40 for PyCharm 4.x).
Each <jdk> element represents single configured interpreter. To remove duplicates simply find elements with subelement <name value="your duplicate name"> and delete entire <jdk> tag.
Sample entry looks like below. (1) in name indicates duplicate.
<jdk version="2"> <name value="Python 2.7.10 (C:\Python27\python.exe) (1)" /> <type value="Python SDK" /> <version value="Python 2.7.10" /> <homePath value="C:\Python27\python.exe" /> (...) // a lot of other fields </jdk>
Answer is based on The mystery of PyCharm and duplicate interpreters blog post.