This is just another example of unintended side effects. When a drug enters the body, it can sometimes have negative side effects that did appear until it actually interacts with the body. Thalidome is far more unstable because of isomerism.
The drug Thalidomide as released in the 1950's is a racemic compound, meaning that it is an equal mixture of 2 different isomers. In this case the two different isomers are called enantiomers, meaning that they have the same chemical bond connectivity but they only differ in spacial arrangement. Enantiomers are mirror images of each other but are not superimposable. In the case of Thalidomide, one of the enantiomeric isomers was safe and effective against nausea and morning sickness but the other isomer is a teratogen, or a chemical that causes birth defects in pregnant women. Many drugs released today are now not mixtures of isomers but instead are composed of a single active isomer.
One possible link between isomerism and the Thalidome case is that the chemical components (isomers) of Thalidome make it possible to refrain the metabolic growth of certain bacteria, while damaging the metabolic processes taking place in human cells. This is what may be the cause of Thalidome causing birth defects in embryos, while preventing the growth of deforming cells in lepers. There must be a chemical interaction between the isomers in Thalidome and the hormones produced by chemical reactions in the human body for it to cause such a disparate reaction.