The original questioner asked the following: What is the kashrus problem with Eida Chareidis Chickens, and why does the Eida think its not a problem? (kikar.co.il/194374.html – @kouty)
However this is unfortunately quite vague. I will therefore explain the situation as I understand it (not based on the article but based on discussions with Rabbonim.)
All chickens receive some sort vaccination when they are born (a few shots actually.) Different hechsherim administer the shots in different places. Some give it in the chest, some in the neck, and some in the leg. The focus of the question is not the location of the shot as that is a different dicussion. The Eidah Charedis gives it always in the leg. This has been common practice by the Eidah Charedis for many years. Recently (in the past month or so) it was discovered by "someone", that a number of chickens (in the 1000s it seems) starting showing signs of illness in the place where the vaccination is given. This caused concerned as it's where the "tzomet hagidim" are and if the tzomet hagidim are torn the chicken is rendered treif (not kosher.) This is a very broad statement as the actual place on the leg of where the tzomet hagidim are found is a maklokes. However simply put if the gidim (which need to be defined as well) are torn, then the animal would be treif. The supposed illness caused by the vaccination (apparently) was cause for concern and made a "ra'uso" (can someone please translate this for me, I can't find the english word best to use?) in the status of the tzomes hagidim and that was the whole cause for concern. The illness didn't cause the gidim to tear (at least I dont' think so) but did cause a change in color or perhaps dis-formation (which I do believe the poskim speak about as raising a cause for concern in the gidim -- in there is a blood clot, etc.)
What came after was a lot of hysteria as it was suspected by some that as many as 90% of the chickens shechted by the Eidah in the last month or so were effected by this. Gatherings of Rabbonim were made to discuss the issue and the Eidah Charedis came out that everything was okay, perhaps even lichatchila, perhaps even mahadrin.
I believe the intention of the questioner was to ask: If the gidim are infected with an illness in some way and have lost their normal look (and are not torn) is this a problem? Is the chicken treif? Is it real cause for concern? Must one be machmir? Why should this be accepted as "kosher lichatchila" or even "mahadrin" as the Eidah seems to be saying. If it's assumed that this illness effected 1000s of chickens then how can we be sure even after inspecting some and discovering no tearing in the tzomes hagidim that others are also not torn? What if some were found to be torn from this disease, would that effect the status of all of them?
(I'll leave it up to the original questioner to decide if this is right or wrong and to then edit the question appropiately, but at least this is a starting put to have the question be taken off hold. I wanted to ask it myself but had to do more research first, however after seeing this I decided to edit it in one shot based on my conversations with Rabbonim in Jerusalem.)