It sounds like you are not doing anything wrong. A walking foot is REALLY needed to do any quilting like SID with the feed dogs up. Even with a walking foot you can get small puckers. You should also try releasing some of the downward pressure that the presser foot is putting on the sandwich. This will also help. The foot is holding back the top layer of the sandwich while the feed dogs are moving the bottom layer forward. Easing the pressure and using a walking foot will make a big improvement. Small puckers won't be very noticeable when the quilt is finished and washed. Don't panic; we've all done this. I did it on a baby quilt after doing many larger quilts.