Basically, as I understand it, when you eat food it goes through your stomach and then it travels through your bowels where the nutrients and water get gradually absorbed along the way. Coffee, as I understand it, stimulates the muscles in the bowels and causes the contents to move through the intestines more quickly. So if drinking coffee means that food will spend less time in the intestines, does that mean that less nutrients will be absorbed from the food than if no coffee was consumed?
Many plants have anti-nutrients, compounds that inhibit absorption of nutrients. Both coffee and tea inhibit absorption of some minerals, such as iron.