I believe I'm coming at this from a different perspective. My husband and I have always had an "open door" policy. Our boys (almost 3 and 5 1/2) begin the night in their bed 99% of the time, and if they wake up in the middle of the night, we just pick them up and put them in bed with us.
So my question for you is, is this a problem for you because picking her up and putting her in bed with you would be disruptive to your (or your husband's) sleep? Or is it a problem for you because "That's just not the way it's supposed to be?" If it's the later, perhaps you could consider the possibility that there isn't really a "problem" exactly. You're all getting enough sleep. She's just sleeping in your bed instead of hers.
Our boys go through phases of coming in to our bed. Most nights, it's just the two of us. I was off for a month for winter break and just started back to work last week. Our youngest has been in our bed a bit lately, and my husband strongly believes that it's because he is transitioning back to going to daycare and just really wants to feel close to us. I think he's right. Our oldest hardly ever comes into our bed ... only when he has a bad dream, and even then he usually goes back to sleep in his own bed.
Try not to worry about setting a bad habit. Habits can be broken, and kids really do go through phases. Right now she needs you. Maybe she can't express her emotions well. Maybe she's not fully aware of what's bothering her and she's just trying to come up with excuses so that you'll comfort her.
Comfort her. Reassure her. Meet her emotional needs. Try not to focus on the fact that she's asking for emotional support at night, and respond as you would if it were daytime. Do what you can to be there for her now, and she really will grow out of this phase and begin sleeping through the night in her own bed.
I guess I'm of the opinion, who cares where everyone sleeps as long as everyone sleeps.
Hang in there! This too shall pass.