Baby hates her crib (and swaddle)?

Charlene

My almost 13 week old baby cries so hard every time she is put down to her crib and put in a swaddle (we use a few different arms up swaddle, including Love to Dream). At night, after the bedtime routine and 40-50 minutes of tears and protest, shushing, patting, pickup-and-put-down, and a pacifier, she can fall asleep and nowadays sleep 5~6 hours for the first stretch and a few more hours after the night feed. In the day time, naps are usually hit or miss...either she gives in and falls asleep or i give in and carry her to sleep...

Is it normal for babies to hate their cribs? Our pediatrician suggests it might be reflux so we are trying different things....but curious whether anybody else has similar experiences?