PX4 PWM Output block was not releasing file descriptors correctly during the disarmed state in SITL mode. Hence it was exhausting all the available file descriptors and causing this issue.
As a workaround,
locate and open the support package root folder using the following command,
>>matlabshared.supportpkg.getSupportPackageRoot
Navigate to toolbox\target\supportpackages\px4\src folder and open MW_PX4_PWM.cpp
After the line 306,
orb_publish(ORB_ID(vehicle_status), vehicle_status_pub, &arm_vehicle_stat);
insert the following line,
orb_unsubscribe(vehicle_status_fd);
Redeploy the model from Simulink.