Someone has said this in my manga.
Does he actually say "two" or "に"? If the latter, why not use 二? I don't see 二つ as being any different.
“2つ” is just another notation for “二つ,” and is read as ふたつ, although some people consider the notation “2つ” as incorrect.
As @Tsuyoshi said,
It's a manga, as you said, and it's very common to have a lot of crappy written Japanese in them (special readings, mix of English, neologisms…). You don't see 2つ being different from 二つ, but the author did. You'll have to ask him why he chose this "spelling".