Emacs  : GNU Emacs 25.2.1 (x86_64-unknown-linux-gnu, GTK+ Version 3.22.16)
 of 2017-07-15
Package: Org-mode version 8.2.10 (release_8.2.10 @ /usr/share/emacs/25.2/lisp/org/)

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With evil-mode enabled (bug still applies without using evil, see: https://github.com/emacs-evil/evil/issues/907), start Emacs, evaluate (setq org-hide-emphasis-markers t).

Open a org file containing the following line:

~$ firejail --get=<id> <file>~

which is shown in the visible buffer as:

$ firejail --get=<id> <file>

Then, visually select via v from the first character "$" to the last character ">" of the line. What's copied into the clipboard is (note the "~" in the beginning):

~$ firejail --get=<id> <file>

instead of:

$ firejail --get=<id> <file>

Also, copying the entire line with V via org-copy-visible will yield ~$ firejail --get=<id> <file>~.

I only use Emacs with evil-mode enabled, so I'm not sure what Emacs equivalents are, but it has the same issue even without using evil according to the evil developer (see github issue posted above).