If you are using the companies by channel option to see where your traffic is coming from you may see some slight discrepancies.
There are multiple reasons as to why there would be a discrepancy. The biggest issue is security.
If your website does not have an SSL certificate and the referral channel is trying to send this info to you, it will fail and the visit will look like it has come to you organically.
Example; Let's assume you have an Adwords campaign running and Google is secure due to having an SSL certificate. Your website is not running a certificate so it is classed as insecure. Google will look at it like this...."I have some secure information that I am being asked to send to an insecure location.....what shall I do?"
It will only send over the information that has no baring on security i.e this visit has come from Google. Obviously in Google to Google (Adwords to Analytics) transactions it will go from secure to secure so you will see your traffic levels accurately.
To best tackle this you should ensure you have a valid certificate on your site.
We are working on ways to tackle this with little work from the consumer side but for the best accurate results ensure you have a valid SSL certificate.