Apparently "Fly Me to the Moon" couldn't be kept for licensing issues (in the US), and they replaced it with a character's theme, if this article is to be believed. That's not everywhere, though:
Every episode of Neon Genesis Evangelion originally ended with an arrangement of “Fly Me to the Moon,” a frequently covered jazz tune written by Bart Howard. Each episode featured a different version of the song, some performed by singer Claire Littley, some by Yoko Takahashi, who also sings the opening-credits banger “A Cruel Angel’s Thesis.”
Netflix’s version of Evangelion — at least in the U.S. — features a portion of Rei’s theme over the closing credits. It’s a dramatic tonal change from the upbeat rhythms of “Fly Me to the Moon” — which itself was often a tonal contrast against the anime’s sometimes dark and depressing cliffhanger endings.
In Japan, “Fly Me to the Moon” appears intact on Netflix, affirming that rights issues led to the track being dropped from streaming in the States.
Netflix’s Evangelion is missing its great end-credits music, Michael McWhertor for Polygon, June 21, 2019