Baytril (enroflaxicin) is a broad spectrum anti-biotic. It is a great anti-biotic and there are members here and other boards that recommend intramuscular injections over oral doses, saying that they personally have had more success using the injections over oral doses. The reactions your vet may have been referring to could be burns from the Baytril on the skin, or if your snake has had some other medication that he administered.
In this case, always follow what your Vet says, if you have any doubts about his prescriptions, get a second opinion with another good vet that specializes in snakes/herps.
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