1) The body discontinuity is because the booster has different diameter from the sustainer.
2) The "Simulation values exceeded limits" is an OR bug, ignore it (because you have no choice )
3) The "recovery device opened while motor is still burning" is because... darnit, I can never figure this one out. I find the deployment settings in OR for multistage rockets to be confusing.
First, each of the motors that you selected have a "P" designator; these are plugged motors, meaning that the motors have no ejection charge. However, on the motor tab, you have selected "Automatic (launch or ejection charge)" for the second stage ignition time. The problem is that neithersecond stage ignition at launchnorsecond stage ignition on prior stage ejection charge is functionally appropriate with plugged motors.
Second, the "Recovery device deployment at high speed (XXX ft/s)" is normal because the sustainer drogue parachute is only intended to slow the descent rate to between 70 and 100 ft/s; the descent rate at the time the main is deployed. The "Ground hit velocity" is the descent rate of the sustainer under the main. The descent rate of the booster is only discernable by looking at the plot.