Das liegt nicht an FileZilla, sondern dem FTProtokoll:
While transferring data over the network, four data types are defined:[2][3][8]
ASCII (TYPE A): Used for text. Data is converted, if needed, from the sending host's character representation to "8-bit ASCII" before transmission, and (again, if necessary) to the receiving host's character representation, including newlines. As a consequence, this mode is inappropriate for files that contain data other than ASCII.
https://en.wikipedia.org/wiki/File_Transfer_Protocol#Data_types
Man kann den Datentyp in FileZilla auf "Binary" festlegen, dann sollte das nicht mehr passieren.