Are they tiny wrinkles along the sewing lines after ironing? Sometimes fabrics shrink at different rates with ironing. it sounds like the fabrics shrank a bit even after you had already ironed them. If you stitch in the ditch along these lines it should disguise the tiny wrinkles.
If they are fold or big wrinkles you may need to adjust the blocks. I think Sharon Schamber has a video on YouTube showing how to shrink a block inside of sashing. Good luck and if you can post a picture maybe someone can give you better advice.