The issue with using g++ in Cygwin stems from the differences in line endings between Windows and Unix/Linux systems, with Windows requiring both carriage return and line feed (CRLF) while Unix uses just line feed (LF). When compiling in Cygwin, the default setting uses Unix-style line endings, which can cause output to appear on a single line in Windows applications like Notepad. To resolve this, users can explicitly include "\r\n" in their output or define a custom ENDL macro to maintain compatibility with standard C++ practices. Additionally, using tools like dos2unix and unix2dos can help manage line endings when transferring files between systems. Overall, avoiding Notepad for viewing files and using appropriate Cygwin tools can mitigate these issues.