It's not a bug per se. It's a shortcoming in their exports. The exports don't specify inside the file which currency is being exported. I think they name the file correctly, but CoinTracking isn't looking at the file name. After you drop the file onto CoinTracking, CT will give you a preview of the import and then you have to push import again to finish. BUT before than last step, there is a pull-down you may not have noticed that lets you select WHICH currency is being imported and the default is BTC (hence the sudden wealth).
What you need to do is click on the pull-down, click the currency this import represents and then click "SAVE". Then finish the import.
It may be simplest to just delete all the imports you have done from wherever and start over.
Steve