I cannot paste text correctly when the content in the Clipboard has been copied from another application.
Old applications may copy text in a legacy encoding instead of Unicode. To paste to EmEditor in the system encoding, use Paste as System Default Encoding which is by default Alt+Ctrl+V. You can find the command in Quick Launch (Help | Search Commands…).
You can make this the default for the paste command by going to Tools | Properties for Current Configuration, open the General page, and check Always Paste as ANSI.