For the browsers:
Shadow dom breaks almost literally everything. It's a parallel world that exists on its own and that needs dozens of additional web standards to patch holes introduced by it. And delays dozens of useful web standards that now have to be aware of it.
On top of that nothing in web components is ever created thinking even one step ahead, and break multiple pieces of basic functionality. It's a collection of barely fitting patches. E.g. at first they couldn't send data in forms. Enter FormData. Oops, still cannot be a custom form submit button. Here's a 7-year old still unresolved issue: https://github.com/WICG/webcomponents/issues/814
For frameworks:
Framework authors have to patch all thise holes on their own. Because unlike web components they actually do care about standards and browser functionality. If styles don't work, forms din't work, code doesn't work etc. because of web components, it's the framework that will be blamed.
It doesn't help that there's an insane amount of work involved in figuring out all the ways they are broken. See for example: https://xcancel.com/Rich_Harris/status/1841467510194843982#m