This old thread describes similar behavior: https://emacs.stackexchange.com/questions/37097/newlines-swallowed-by-org-capture
Basically, the last position in the narrowed org-capture is actually the first position on the next line, so when you go to (end-of-buffer) and start typing you start clobbering the next headline. I tested this with emacs -Q, capturing an `entry` with `file+headline` in org 9.3 and it was working as expected, then in that same session loaded 9.3.6 and the capture buffer was one character longer (the added newline at the end) enabling the clobbering behavior.
