There are many factors taken into account for the contacts 3D Touching on the Messages app.
It bases its suggestions by time, day and your location.
Say you only text someone while you're at work, during normal work hours, Monday-Friday. If you're at home in the evening (or any time during a weekend) it is more likely to not suggest that person, since you only text that person on a week day during the day while at work.
It's a little more complicated than just recents. It may look very random at a glance. But what you see is based off the time, day and your location.