You're right - you should have asked about the price going in, but I understand why you didn't, based on your past experience. I don't feel 3 cents per square inch is too high for custom quilting, particularly if they supply the batting and thread (you didn't say whether they do or not).
However, they did NOT do what you asked, and that is unacceptable. In that case, I would expect them to remove the stitching in those areas and re-quilt it, particularly if your instructions were in writing.
If you had given them the freedom to do whatever they wanted and you simply didn't like it, that would be a different story. In that case, they might offer to re-quilt it (although they really wouldn't be obligated to), but only if you removed all the quilting first.
I hope you can get it worked out with the quilter - I'm sure she feels bad about it too (we don't know what happened on their end to create the misunderstanding). Let us know how it all works out.