Every time, I’d download a file from FileZilla, it would have extra blank lines. The number of those lines, would increase as many times as I’d download and reupload the same file. A css file that was less than 500 lines of code, ended up at 11,000 lines after few updates. You can imagine, how confused I got from all that mess.
The solution was piece of cake. Open up your FileZilla. Navigate to the Transfer tab, from there choose Transfer type and change from Auto (default) to Binary.
Because, the website I was working with was build on WordPress, I first started searching for the problem there. I checked if it was the “Update” button from the theme editor in the Dashboard, than I tried with another theme, as I thought it could be the functions.php. But, at the end it appeared that it was just wrongly configured settings in FileZilla. I guess, things screwed up after an update. Yet, my brother who is on Linux, doesn’t have this problem, but he uses the same default settings as me.