Apple mail sends non junk to junk folder

I have a variety of email accounts: iCloud, local pop, hotmail & gmail. Every time I log onto Apple Mail, I check my Junk folder first to see if there are any inappropriate emails I need to block and for emails marked as junk when they should not be. I also am finding some emails placed there that have not been marked junk. Today I found 3 that were especially upsetting. One was from Apple telling me about a recent purchase, another was from a trusted and often used purchasing site and a third was an important email from my pension source. All of the sources of these emails have been received in the past with no problem, but today I see them in my junk folder, yet they are still black in color and I can't mark them as NOT JUNK because they were not marked as that. How do I keep good emails from being placed in the junk folder when they have not been marked as junk?