You should be able to combine blocks from the CARNOT Toolbox and (custom) Simscape blocks.
I don't have Simscape so your model wouldn't help. But you should provide more information. Which state functions are you trying to exchange between the blocks and which solvers did you use? Did you try to put the Simscape blocks into a model reference subsystem? Did you try to update/run the components individually? Like running the Simscape blocks by their own, if need be with some dummy inputs connected?