Your post and profile don't mention where you're located, but there are likely chicken keepers in your area that can help you assess your coop's security. It's not easy to explain coop security and construction via an online forum. Though it sounds like you have most of the bases covered, it might be worth your time to enlist some friendly help to identify areas where you have potential security issues.
In this case, I think you forgot to check that everyone was up for the night. That's obviously not a coop/run issue, but something that MUST be done EVERY night. Doing a head-count is important too. We've had birds wander around so much at dusk that they forget to go in from time to time, then can't find their way once the sun goes down. It happens, but we catch it with the head-count, and pull out the flashlights if we can't see them close by.
As for sick birds, I don't know what your post history is on this forum, but come here right away any time you have a health issue with your birds and a vet is not an option. There are dozens and dozens of VERY knowledgeable folks that are more than willing to help you diagnose and recommend treatment options for ailing birds. I'm sure you keep a close eye on your birds' health, and it's super-important to get them treatment fast. Why? Birds are usually on the last of the downward slide when we recognize a problem because they hide their health issues incredibly well. It's a defense mechanism. So, treatment needs to be started ASAP in most cases to help them recover.
In the end, we all lose birds from time to time. I'd encourage you to not dwell on the lost birds, but celebrate the good lives they had while with you. It's happened to all of us, and if there is someone here that hasn't lost a bird, they probably haven't been keeping them very long.......
