The BOM is generated by, say, File.WriteAllText() or StreamWriter when you don’t specify an Encoding. The default is to use the UTF8 encoding and generate a BOM. You can tell the java compiler about this with its -encoding command line option.
The path of least resistance is to avoid generating the BOM. Do so by specifying System.Text.Encoding.Default, that will write the file with the characters in the default code page of your operating system and doesn’t write a BOM. Use the File.WriteAllText(String, String, Encoding) overload or the StreamWriter(String, Boolean, Encoding) constructor.
Just make sure that the file you create doesn’t get compiled by a machine in another corner of the world. It will produce mojibake.