I ran into this issue while developing https://www.faceshapeapp.com where user uploads their photo and face detector is run on top of the picture. Shortly after launching about 10% of users complained having rotated images, after some debugging, I discovered that it was due to exif rotation.

You could parse the exif and rotate the image using canvas, but thankfully, there's already a JS library which does it for you: https://github.com/blueimp/JavaScript-Load-Image.