An informal phrase meaning “I don't mind” or “that's fine by me”; can also carry nuance of indifference, reluctance, or mild annoyance depending on context.
別にいいけど、行くなら気をつけてね。
I don't mind, but if you go, be careful.
それで決めるなら別にいいけど、私は反対じゃないよ。
If you're going to decide that way, fine by me—I don't oppose it.
別にいいけど、そう言われると気分はよくない。
I don't really mind, but being told that makes me feel bad.