Phytic acid in hulls of nuts, seeds, and grains prevents absorption of various minerals. Flavonoids are quite common and remove (chelate) such metals as iron and zinc. Oxalic acid and oxalates in tea, spinach, and a few other veggies block calcium absorption. Glucosinolates found in many cruciferous veggies will block iodine and contribute to goiters. Protease inhibitors sabotage digestion and absorption of protein in the gut. Lipase inhibitors do so to fats. Many beans have amylase inhibitors, saboteurs of the conversion of complex carbs (starches) into simple sugars(1). There are numbers of others.
Excessive amounts of various nutrients can turn antinutrient. Way too much fiber is not seen very much in actuality yet could potentially make food move through the intestines too fast too absorb nutrients properly. Calcium taken along with iron can inhibit a transport protein and thus absorption of iron(1).
Of course, all this doesn't mean we can't eat, in particular eat right. Western-style diets mean tons of processed foods [and much less emphasis on fruits and veggies] and messed-up gut health. Many just plain don't have the right mixes of beneficial microbes, which means less absorption of nutrients period as well as freer reign for antinutrients(2). Sprouting, fermenting, and cooking all reduce different antinutrients(1) - though cooking tends to reduce varying amounts of good nutrients too.
Sources:
1. "Antinutrient." Wikipedia, The Free Encyclopedia. Wikipedia, The Free Encyclopedia, 26 Jan. 2019. Web. 16 Apr. 2019, https://en.wikipedia.org/wiki/Antinutrient
2. "Are You Getting Enough Nutrition From the Food You Eat?" Isagenix Health, Isagenix Worldwide, Inc., 7 January 2018, https://www.isagenixhealth.net/are-you-getting-enough-nutrition-from-the-food-you-eat/