"Come between" (without "in") is an expression that means to interfere in someone else's romance or to break up a pair of lovers. For example, "If you come between my best friend and her fiance 💑, I will make your life miserable."

---

Literally, "come in between" would mean "enter between," e.g., "I want you to come in between noon and 2 pm." (This sentence means "I want you to arrive at work between 12 and 2 pm.")