It shouldn’t be. But there are 2 commands that may get confused: 1) insert citation; 2) insert literature note link. A new lit note is created if you click on the link inserted in the second case.
So, you should check how your hotkeys are set up. For me, ctr+shift+E is the literature note command (NOT the citation command), so if it’s set up the same way for you too, then that’s why.