It was in my junk mail. Sorry I didn't realize that.
Your email ended up in my junk mail for some reason and I didn't see it. Sorry about that.
この場合、次のような言い方ができます。
ーIt was in my junk mail. Sorry I didn't realize that.
「迷惑メールに入ってた。気がつかなくてごめんね」
ーYour email ended up in my junk mail for some reason and I didn't see it. Sorry about that.
「なぜか迷惑メールに入ってしまってて、気がつかなかった。ごめんね」
メールが迷惑メールボックスに入っていたことは in one's junk mail のように言うと良いでしょう。
ご参考まで!