When I run M-! enter shell command enter in org mode, I expect the output to be inserted into the buffer I have active.
Instead, emacs opens a second buffer (splitting the window in two) and inserts the output there. How can I make it insert the result in the buffer I am working?
This is the normal behaviour for shell-command.
If you want the output inserted into the current buffer, you must supply an argument (like C-u M-!).
You can do that by typing C-u M-! command RET. Checking the help on M-! explains why it works.
M-! runs the command shell-command, which is an interactive compiled Lisp function in `simple.el'. It is bound to s-L, M-!, <menu-bar> <tools> <shell>. (shell-command COMMAND &optional OUTPUT-BUFFER ERROR-BUFFER) Execute string COMMAND in inferior shell; display output, if any. With prefix argument, insert the COMMAND's output at point. 