If you look at
you see that some languages are listed twice. Like English, German, Russian and Chinese. I had this happen for some time now and my guess is that if someone translates multiple files on Transifex in a short time, like when updating only a few strings in multiple files, then the webhooks fires to fast and cTransifex gets confused. But that's just a guess
Usually I was able to just recreate the files using the "Get Data" button in the backend. But when I tried to do that today the button did nothing. In fact the whole modal goes through the roof (only partially visible on top) when opening. It comes back to normal when I resize the browser to a smaller width. But clicking the "Get Data" button seems to do nothing at all.
Tested using IE11 and Chrome on Joomla 3.1.5.
Using the developer tools I see that the button requests the link "administrator/index.php?option=com_ctransifex&task=transifex.resources&format=raw" and stays at "pending".
Concerning the duplicate translations - I occationally see this on our VirtueMart translations download page, too. Today I've taken a screenshot of a translation that showed up four times and also cut out a few lines from the the file com_ctransifex.error.php, which looked like being related to that issue. I don't understand this kind of stuff, but maybe it gives you a hint what is going on there.
I've attached a zip file holding the cutout from the log file and the screenshot.