Hello @Birand_Bilgin_Ozer,
Unix and Mac use new line, Windows uses newline/carriage return. I have experienced the same issue using Visual Studio as opposed to MonoDevelop, this was on Windows, which I am assuming you are using also.
This article has some information which may help, there are some options within MonoDevelop that you can change.
In Visual Studio I will experience this each time I create a new script from Unity. The templates uses within MonoDevelop I believe are saved with Unix/Mac formatting. You can edit these templates, correcting the line endings which should mean that going forward you don’t have to keep making any changes, I’ve not done this myself yet as I am aware of the issue and its not a big problem to change the line ending settings from Visual Studio each time I need to.
Hope this information is of use.