I had updated certs late last night and had a ton of issues getting through the scripts. My internal scripts generate 10 SAN certs covering approximately 50 domains in each.
Here are the various Lets Encrypt internal errors I saw last night in the several runs I had to execute to get it to complete:
I should have mentioned in my OP that I was able to get my scripts to complete after I babysat and re-ran them for 3.5 hours last night. I had to run my scripts 18 times. Some issues of my issues were appear to be related to DNS propagation delays.
Due to the size of each certificate and the limitations of the Godaddy DNS API, it takes quite a bit of time to get through each certificate. A test run this morning shows 700 seconds per certificate! I suspect that this is a contributing factor to the various LE internal 500 errors.
Another point, these errors have always occurred with my big SAN certs with LE but last night was extraordinary. I wonder if the LE servers were under a big load last night?