It is because you are alternating between the two and they have different line break settings.
The issue can be corrected in filezilla, but the files you have already uploaded with filezilla will have the problem when downloaded with Dreamweaver:
Edit your Filezilla FTP client default transfer mode, by default it is "Auto", update it into "binary".
If you google "extra line breaks filezilla" you will find a lot of posts about it.