I'm not sure for this issue but in my case I have a custom code running on the minicart
<preference for="\Magento\Checkout\CustomerData\Cart" type="\Vendor\QuickCart\Model\CustomerData\Cart"/>
In my case I'm extending the method getSortedCartItems
and doing my own work in there.
So either the issue comes form a custom code broken there either you can analyse the getSortedCartItems from Magento Checkout and see what is happening.
Worst case scenario you can always extend the method to clean the returned array by yourself...even if for sure that's not the best solution.