Internal SD card accessible through PC even after encryption I recently bought a OnePlus Two. The first thing I did after getting the new phone was a full encryption under security settings. 

But even after that, the files in my internal SD card, such as  WhatsApp media files, images and more are accessible via a PC. 

How to prevent this? Am I missing something?
You can't prevent that. It is because your device is mounted to the computer via MTP. It's supposed to be visible. However, whenever you boot up, a password will be required to decrypt your device before any data can be accessed, so you need not worry. Also, MTP connections won't display any data if the device is locked. This is a security measure. In Lollipop, not even a factory reset can remove your lock.