Filezilla seems to have an issue when downloading files in different encoding formats. In short, when you upload files using the client in ASCII or UTF mode, different platforms can handle line breaks within the files differently. The result of this is lots of superfluous line breaks across all of your files.
Fortunately this behavious can be changed easily, and to fix the issue you need to set the default data transfer type to Binary. With this changed your FTP client isn't processing the files you download based on their content:
Edit > Settings > Transfers > File Types > Default transfer type > Binary #ftp
Here is a nice video demonstrating how this can be done:
However, if you are deploying source code to a live website then FTP may not be the best solution. We would recommend that instead you consider using a more mature version control process such as GIT.