I worry about breaking something serious on the MR-1. Since first plugging in my MR-1, I’ve broken six mills and busted off the finger of the tool probe. I’ve crashed a tool into a piece of stock and into the (x-tall) probe base. So far, none of these incidents seems to have caused any serious/lasting damage.
Are there things I could accidentally do that would cause permanent/serious damage to the spindle, the motors, the lead screws? Or anything else?
Sounds like you’re learning the hard way. Check it twice, cut once applies here. Then again, we tend to learn very quickly when the $90 endmill skeletons start piling up. To answer your question, I am quite sure it can be broken very quickly.
The spindle will fault if it stalls for too long, and requires a power cycle to come back. That is better than burning up.
The steppers will probably stall long before breaking, but I don’t think it’s a good idea to try.
A big crash could cause the machine to come out of tram, and it’s good to test that once in a while using the same instructions as in the setup manual.
Overall the stock machine has pretty low travel rates which should keep it less likely to self destruct. There are obviously threads on here about how to increase that, and I have, but I also assume that I’m outside of any warranty.
I feel like I’m through the worst of it. I just finished an op that ran for an hour and I turned my back on it after only about 1 minute. 
Good to know. I’m looking forward to some upgrade mods someday. But for now I feel like I have some runway ahead of me.
I think itll take a pretty big crash, the frame is fairly stout and as others have said the spindle errors out on stall and needs a hard reset. Ive stalled mine a few times and i burned 2 60 dollar 1/2 end mills because i was running it to hard in 4140 prehard. I just buried a radius mill and im still trying to figure that one out.
I think if you dont have the soft stops enabled youll find out quick how easy it is to break. That would be the number one thing. 100 ipm right into the front towers. Ya thats breaking something. Most of the skills to not break things is just muscle memory. Check your probe, go slow on the first pass or do a dry run, dont operate outside the normal feeds and speeds of the machine. 1/2 endmill at 8k rpm and 100 ipm in stainless isnt a good idea.
Stalling the spindle has been the only thing thats cause me some issues on the machine. Nothing major, and I always stand by the machine if I’m running something with a heavy load. The plus side to a cnc for me is being able to have it running while I do other things in the shop or run a different machine while the MR1 is humming away. For that reason I generally don’t program in a way that is going to load the tools up enough to potentially stall.
With the machine being pretty DIY it’s easy enough to straighten things back out if you have a decent bump though. I may have had to resquare my gantry a time or two when I was finding the limits in stainless. 