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The best thing to do in any new relationship is to take it slow and approach it with caution. Also, from the start being honest and genuine is helpful so the other person in question does not get confused later on.
So little steps at the beginning and see how she responds and that will be a clue as to how to proceed.
You were honest (so, you got to see how she is)
Perhaps now you can keep it a low key and see what comes out of her.
People can play mental games just for so long and then their true self comes out.
You want to see what the real person is (then you would also know more about your own intent and feelings) If possible, just go with the flow and let her tell you what she wants. Women know what they want and a lot of them will go to an extent to get it. Unfortunately,, a lot of women don't say it out straight and hope that the guy would guess it. So, if you can don't try to guess and ask her if you're not sure what she wants.
If you are willing to take a chance and ask her out (the interaction at work does not always allow for much anything or to get to know someone better)
Even if it is asking her to eat lunch together during a break (preferably not at the work setting though) This will allow for more time to become familiar with one another on a personal level (not just as coworkers)
Even shy women like positive attention.
It seem that you know where you stand. There is nothing you can do to speed up her response. If things are to happen they will. Just keep your expectations realistic so you don't get disappointed.
You could phrase it like "If you feel like getting a cup of coffee or a bite you have my number" That at least leaves it open to her and I think if she wants to do it, it won't be too long from when you asked. Some women do date more than one men. You may not be able to know unless she tells you she's seeing someone (but if she does tell you that, it would indicate either - this is the truth, or she is not interested)
Maybe if you play hard to get she can get interested then (if meant to happen)
Some time friends would have your best interested at hand so, it does not hurt to see what their take is on this (like you already mentioned what they've shared with you)
Only she knows why she did so. If you speculate about the reasons you would get yourself in tangled in it.
If there are some coworkers with which the two of you are friends with, perhaps going out for a snack with few other people and she, may not be threatening to her. As far as why she turned you down that is also a speculation; afterall, you can still talk to her and she to you. Affection is stronger than grudges.