The argument concerns abnormalities that are caused only be elevated hormonal activity. Other abnormalities don’t have any impact on the reasoning.

If elevated hormonal activity can result from things besides industrial by-products, then the elevated hormonal activity that the reptiles in the swamp have does not prove that there are industrial by-products in the swamp. The elevated hormones might result from other things.

The author doesn’t make any assumption about exactly how the by-products got into the reptiles in the swamp. Maybe the reptiles ate food in the swamp, and that food contained the by-products. This doesn’t undermine the author’s reasoning.

We know there are reptiles in the swamp with the abnormalities that are only caused by elevated hormonal activity. Whether there are other reptiles that have those abnormalities or not has no impact on the reasoning.

The conclusion doesn’t concern alligators in general. So there’s nothing flawed about relying on evidence drawn from a sample of alligators in the swamp.