First of all, welcome to the Buttonizer Community 🙂
Buttonizer should work together with Elementor, we're using Buttonizer on many customer sites which are built on Elementor too. Buttonizer does only have CSS for it's own classnames and should not alter any other theme settings.
The other way around it is possible for themes to change the style of a Buttonizer menu, but we're trying to make the impact as little as possible.
Can you might let us know what your site is? Then we can take a look at it and see what's happening. Do you still have Buttonizer installed?