After searching around much more I found that adding a memory block to the outputs sent to Simulink solves the issues.
How to use Classic State Machine outputs in Simulink?
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I created a classic State Machine using the StateFlow add-on to Simulink. I am able to input various parameters that are updated in my Simulink model, but I am unable to take the outputs of the State Machine and use it elsewhere in my Simulink file. I get an error saying 'UAV_SIM_MAIN_7_0/DECISION ENGINE1/DECISION ENGINE' updates persistent or state variables while computing outputs, therefore it cannot be used in an algebraic loop. However, it is in a loop with the following blocks. For more information, see Algebraic Loops with MATLAB Function and Stateflow Blocks.' I tried changing the State Machine type to a Moore Chart but it does not work with the setup I have with my current State Machine. Is there a way to modify my classic State Machine to allow for its outputs to be used elsewhere in my Simulink model?