When you use carrier flat rate packaging you need to make sure you select the correct carrier packaging and service. If you just pick a custom box and enter the dimensions, then you are not setting up your label correctly and will not be paying the correct postage when you purchase the label.
We are seeing the same issue. The post office charging adjusted rates saying the weight was off by 3 lbs on a order that had 1 shirt and weighed .75 ounces. There is no way! Then they charged us more for a package that they say we missed measured, they say it was smaller than we stated and then charged us more.
This is a open check book for the post office!!!
I just noticed this thing in my account too. I feel like a completely rip off from Shopify after they calculate shipping for a customer then they come back with a shipping price adjustment and also without inform me at all if I don't check the bill I don't see this. Stop scam customers please