I also experienced that problem. When using the MATLAB Function block, I learned to always define the size of the inputs and outputs to avoid any trouble.
To do so:
- right-click on your block
- explore (it opens the Model Explorer directly at the right place)
- you should see the list of inputs and output of your MATLAB Function in the central part of the window
- For each variable:
- Click on it
- Set the variable size on the right part of the window
- Click on Apply button
- Once you have set all variables, you can close the Model Explorer and tada, it should work!