Why is the use of pesticides such as DDT being discouraged in many countries?

There are SO many reasons. Basically it affected fish, animals that ate the fish, humans, and especially bats. It even hurt microorganisms badly causing pour conditions for the animals who needed the organisms, them being plankton, algae, and mostly water based microorganisms.

As you can see, it was because it was a serious health concern, for it got into the water and harmed living organisms from there.

DDT was banned in the United States when it was discovered that bald eagle populations and alligator populations were dying off due to extremely fragile egg shells and lack of sexual development. Since then, DDT specifically and similar organochlorine compounds have been linked to Diabetes, gynomastia (male breasts), polycystic ovarian syndrome, certain autoimmune disorders, male and female infertility, low progesterone, and cancers such as liver, uterine, breast, and prostate. A number of studies from the US, Canada, and Sweden have found that the prevalence of diabetes in a population increases with serum DDT levels. Studies in the US, Australia, and Germany are also finding that the prevalence of polycystic ovarian syndrome and similar male anti-androgenic disorders in a population increases with serum levels of DDT. Studies in China showed there was a positive, monotonic, exposure-response association between preconception serum total DDT and subsequent early pregnancy losses. DDT is also showing to be no longer effective against malaria-bearing mosquitoes due to DDT-resistant "superbugs" appearing throughout parts of Africa, Asia, and parts of Central America. Unfortunately, DDT is still being used in countries that export food to the US, Europe, and Canada.