Same problem with 6s. Gone from contact list. Usually don't notice until I go for the person in contact list. They're gone.
I don't know what to tell you because I have yet to lose any of the contacts I have on my iPhone. In fact, I don't recall any of them randomly disappearing from any of the previous iPhones I've owned over the years. With that in mind, are the contacts associated with iCloud or another email account? Have you tried the following?
1. Initiate the Contacts app.
2. Select "Groups" in the upper left corner.
3. Tap each item therein to make sure a check mark appears next to them.
4. Select "Done" and then check to see if your missing contacts reappear.