You appear to be setting environment variables (“PATH” “MANPATH”) in your .bashrc or .zshrc: those files are only read by interactive shells, so you should instead set environment variables in startup files like .profile, .bash_profile or .zshenv. Refer to your shell’s man page for more info. Customize
exec-path-from-shell-arguments' to remove "-i" when done, or disableexec-path-from-shell-check-startup-files’ to disable this message. For information about GNU Emacs and the GNU system, type C-h C-a.