Employees often visit the website of the company they work for. If you don’t have the IP filtered in your web analytics tool they will end up counting as part of the direct traffic. As a rule of thumb, filter out all the IPs of the company’s employees.
Often one of the main culprits of distorting direct traffic figures are having an intranet or customer portal integrated with your website. In this case, it is not advisable to filter out this traffic completely, but to set up different views within Google Analytics to see the data without this traffic.
It is quite common for Outlook email clicks, or mobile device app clicks to not pass referral information. You can usually identify if an email has caused a spike in direct traffic by analyzing the traffic around the time a particular email was sent but it can be impossible to track when we are talking about hundreds of employees sending emails every day.
Programs such as Skype, Slack, asana, or news apps often do not pass referral information and therefore result in direct traffic. The best way to capture and analyze this is to understand where your website links are commonly used or where they are digitally placed, including apps.