DS was doing this every. single. day. for about 2wks recently (he's now 9 w). It drove me crazy cuz he wasn't getting enough rest and he'd be fussy all. day. long.
Took me forever to decipher his problem... 1) he wasn't always swaddle; he'd wake himself up (but you said your DD is swaddled), and
2) He has a gas bubble that didn't come up w/burping. The gas bubble makes him uncomfortable so he'd semi-wake and grunt/fuss/wriggle. It's also worse when he is flat. So nowadays I try to burp him as best I could, and if I see him doing this waking thing every 5 minutes, I'll pick him up and burp him again. usually I can get a big burp with 1 or 2 tries, and then he'll be able to go into deep sleep for 2 hours. GL!