This is likely due to Edit-Time Checking being enabled on the model. If the model has been saved with Edit-Time Checking enabled, then Edit-Time Checking will remain enabled when the model is re-opened. This will check out a Simulink Check license.
There are two functions you can use to address this:
edittime.getAdvisorChecking determines whether Edit-Time Checking is on for a model
edittime.setAdvisorChecking can be used to turn Edit-Time Checking on or off for a model
Note that if you disable Edit-Time Checking for a model via a script, users who open the model might not be aware Edit-Time Checking has been disabled.