Looking for reason my Shapeoko did something I didn’t expect. I had made a couple of vegetable trays and all went well. Then the other day I was making another and the first partition was cut out as it should, then when I started the next partition the router took a dive into and through the 3/4 inch board in about 10 seconds, leaving an approximate 1 inch hole.
The SO3 is a very good machine but it is all belt driven. So depending on your F&S you can come off the rails and you get your problem.
Check all your v-wheels for cleanliness and the rails. Check their adjustment by lifting each end of the gantry and you should have no slack. Lift the Z and there should be no slack. If either lift then adjust your v-wheels. Look at your belts closely and depending on what model you have basically your finger should fit tightly under the belt at the half way point.
Power off your SO3 and manually and slowly move your gantry forward and back a few times. If you find any tight spots address that. Then move the Z carriage back left and right a few times and same check for any tight spots.
Vacuum hoses that get tangled up can cause you to loose steps. Also your router cord can get tangled up on the top of the gantry and cause you to loose steps.
When moving the gantry around manually go slow. If you move it too fast you will get a grinding noise caused by EMF generated by the stepper motors. It will not hurt anything but go slow to avoid the EMF.
@WillAdams asked what Z you have. There are 3 possible for an SO3. The belt Z was the original an was on early machines. Then they came out with the Z-Plus and later the HDZ. The Z-Plus and HDZ are ball screw driven and have linear bearings that need periodic maintenance of cleaning the rails and oiling the bearings. A Z-Plus or the HDZ can cause loss of steps when they dry out. You use Mobil Vactra #2 oil for the lubrication. It is sometimes called way oil and is used on heavy duty mills and lathes to oil the moving parts. C3D sells small bottles or you can buy it on etsy.com. People in Canada seem to have a hard time getting the oil because of import/taxes and shipping but it is available.
Come back after your diagnose your problem and get more help or let us know what fixed your machine.