The nature of baby sleep changes at 12 weeks. Her sleep cycle is now like ours.
In the next few months, you need to teach her to self-sooth herself to sleep. They will pop up and scream as soon as you put them down until you teach them to relax when you put them down. There are lot of ways to teach her to be able to put herself to sleep. Some use the swing until 6 months and don't worry about it. I nursed until drowsy, put down, and repeated until they would roll over to sleep. I also introduced a transitional object at 10 weeks. I also used the 5 minute startle to reset the sleep cycle (5 minutes before they usually wake up from their nap, you go in and startle them enough that they roll over, this resets the sleep cycle and helps them to learn to consolidate their naps.)
My first nursed every 2 hours until 12 months. My second was a good sleep coming out of the box, but he became a great sleeper after taking the time to teach him to sleep. It took me 3 months, very little crying, but it worked. I used a bunch of different methods, but I started at 12 weeks with nursing till drowsy and then putting in crib. It would sometimes take 5 or 6 attempts before he would let me put him down, but within a few weeks, I could just put him down. It also didn't impact his night sleep. He had a good solid block before wanting to nurse at night. And then at 6 months, I used the baby whisperer hold CIO method to get him to skip his first feeding. So he only woke once a night.
12 weeks is to young to CIO and you will break trust and make her scared of her crib.
She is popping awake, btw, because she is overtired. Start trying to put her to bed earlier, by 15 minute increments.