This post currently has several different claims:
The OP claims the taste, size and appearance of the eggs are different. I'm not addressing that claim.
"People from the chicken industry" claim that this is because of chickens eating eat others droppings. I'm not addressing that claim because even if it is true (i.e. caged chickens eat less droppings and also that that leads to changes in the egg), I don't see any claim that this makes the eggs dangerous.
Finally, there is the main claim: free-range chickens have higher dioxin contamination, which is a safety issue. This is the claim I am addressing.
The dioxin claim is reproduced in this article:
Contamination of free-range chicken eggs with dioxins and dioxin-like polychlorinated biphenyls, Greet Schoeters, Ron Hoogenboom, Molecular Nutrition & Food Research (Special Issue: Dioxins), Volume 50, Issue 10, pages 908–914, October 2006 DOI: 10.1002/mnfr.200500201
In their abstract, first they argue the need for care:
Dioxins and dioxin-like (DL) polychlorinated biphenyls (PCB) are persistent organic pollutants that enter the body mainly by food intake. A small margin exists between current exposure levels in the human population and the levels causing biological effects. Therefore, stringent control of concentrations of these contaminants in food and feed is needed.
Then they claim that free-range chickens are a concern:
Eggs from free-range chicken are increasingly becoming an important part of the diet. These eggs have a higher risk of being contaminated with increased levels of dioxins and DL-PCB than barn or cage eggs. Ingestion of soil particles from environmentally contaminated areas may contribute to elevated dioxin levels in free-range chicken eggs. Available data show that current soil levels of dioxins and DL-PCB in residential and agricultural areas in Europe often appear to be too high to produce free-range eggs with dioxin levels below the current limit values in the EU.
Then they admit that it might not be a concern for the eggs:
On the other hand, polychlorinated dibenzo-p-dioxins/polychlorinated dibenzofurans concentrations in eggs from free-range chicken are not necessarily above the limit values.
Finally they urge caution:
Contamination levels in soil should be kept low and should be controlled in areas with free foraging chicken although all modifying factors that influence uptake of dioxins and PCB from the environment and transfer into eggs are yet not well understood.
The article is behind a firewall, and the abstract provides no way of seeing how they reached their conclusions. How do we know they are not egg-industry shills?
Well, this paper supports their claims about eggs picking up contaminants from the soil:
F. Schuler, P. Schmid, Ch. Schlatter, The transfer of polychlorinated dibenzo-p-dioxins and dibenzofurans from soil into eggs of foraging chicken, Chemosphere, Volume 34, Issue 4, February 1997, Pages 711-718, ISSN 0045-6535, 10.1016/S0045-6535(97)00463-3