Lost, confused and feeling like a failure

Bug's 12 month check up was Monday (even though she is now 13 1/2 months old). I am still a little emotional about the whole situation. Bug's weight is of MAJOR concern. She has always been tiny but between her 9 month checkup and now she has gain ONE pound!!! I feed her 3 meals a day plus 2 snacks and she eats nearly everything. When we met with the doctor in May he said Bug would be fine to switch to whole milk at 12 months. Just make sure a little at a time and monitor her. So about 2-3 weeks after her first birthday we started the switch to milk with what I thought were no problems. The doctor thinks that Bug either has a milk allergy, lactose intolerance or she might be allergic to gluten. Since she has been on milk for less time than the wheat, he told me to pull her off milk and switch her to soy formula for the next month to see if that helps her weight gain at all. I'm just so confused, depressed and guilty about everything. I feel like I did something wrong. Like I don't feed her enough, even though I KNOW she is well-fed. That my breastmilk didn't have enough calories for her little body (already a concern the doctor expressed in the past). I just want her to be healthy and I love her so much but it sucks not knowing what is causing her slow growth.