She seems to use it as if it's a conversation filler, and I never really understood what it meant.
When I asked what she means by that, she says it's like "something between us". I just nodded and said "Ohhh" but I didn't really understand.
She doesn't use it in chats or text, but I just notice that she says it out of habit during conversations. What does it mean?
As @virmaior suggested in the comment, it's likely that you've misheard なんか（何か）, which is an informal contraction of なにか or なんだか.
Basically なんか can be used in the same way as なにか, but なんか very often precedes an adjective/adverb to add a 'somewhat' or 'kinda' nuance:
- なんか食べるもの = なにか食べるもの something to eat
- なんか変 = なにか変 kinda odd
Sometimes it's used on its own as an equivalent of なんだか, meaning "not sure but ...", "dunno why but ..." or "somehow":
- なんか、あの2人って仲いいよね。 Somehow they're geting along well, aren't they?
- なんか、急に怒り出した。 Dunno why but (he) suddenly fell into a rage.
なんか as a truly meaningless filler (i.e. as an equivalent of "er..." or "well...") is not very common, but it's mainly used by some people, especially by younger females. Some people do have a habit of saying this very often, but many people frown upon such usage.
- ってゆっか～、なんか～、超ダサいってゆっか～ (I don't know how to translate this...)
Finally, as for "something between us", maybe your friend was trying to describe the definition of 仲【なか】 (personal relationship / term), which is not relevant.
