Yes....
The chlorine itself breaks down into simple water and salt... The issue is the by-products that chlorine tags along with it, but these are mainly seen in paper mills. They bleach the the paper white... such as your coffee filters, papers, toilet paper, paper towels... ect. These toxins are called dioxins. However they are even seen in our drinking water (or the water the birds are soaked in) Chlorine reacts with organic substances (bacteria) causing formation of these so called dioxins or another one that you may be familiar with is chloroform.
Chlorine is a man made product... and it has several forms. When dealing with chemistry it only takes an electron to change an element or a compound... so it's very easy to have multiple compounds containing chlorine. Chlorine is used in it's pure form to clean the water... when added to pools there is other elements with it (more chemicals). Another is example is Hydrogen Chloride... which when it's mixed with water creates hydrochloric acid which will burn your skin.
It's too complicated for me to understand and I took a couple chem classes. I have a couple of folders full of notes and that I kept.... never thought I would use them on BYC! SO my info may not be up to day or a bit twisted but I think you catch my gist...
They say chlorine is safe... but the government also says a lot of things are safe which I think is bogus. It's just one of those things that you get when you mechanically process an animal.... but the thing is they don't have to use Chlorine, they can use a handful of other things that will do the same thing... but it just cost more. God forbid if we have to pay an extra 10 cents a pound for clean chicken.