You need to ask her because only she has the reason why she does it. Why anyone else would/has done it is really irrelevant.
And to be honest, the only question you need to be asking her is "why are you calling me every night at this hour?" That's not a clingy question--that's a question to elicit clarification from her. I mean, what are her intentions in doing this? Is the reason that she regrets what she did in breaking up with your or is the reason that she's an attention monger and needs every guy she knows to validate her worthiness? Did things with her new boyfriend not work out and she's using you to mark time until a new guy surfaces?
There are a gazillion reasons for someone making these late night calls and we can speculate on it til times get better--the person with the answers is her and you need to point blank ask her what her intentions are with these late night calls, if you're that curious.
People treat you the way they feel about you
If you choose to remain with someone who doesn't treat you well, you cease being the victim and become the volunteer.
~Derrick Jaxn -- look him up