there are lots of possible reasons for that...
1.) gas- however, if this is it, she usually would keep on crying until you get to massage her tummy downward and then she farts... do you burp her every time you feed her?
2.) might be having a cold? usually the reason why a baby wakes up every now and then is because she's feeling something or she's having a hard time with something... does she have a cold?
3.) teething- she might be having teeth, does she experience multiple bowel movement in a day unlike the usual? or does she have a fever? these might be signs of her teeth coming out... look at her gums for some whitish teeth about to pop out.
4.)how's the room temperature? when my daughter was 3 months old, she kept crying one night and it all got us scared... when we felt her legs and arms, it was cold..so we wrapped her warm, and everything went fine....
5.) hungry- she might be hungry, give her some milk... she quiets down to your pacifier, but she might be hungry, that's why she cries...?
well, these have been my experiences with my daughter, she is a year and 4 months now. congratulations on your newborn.