If I am doing backups from LVM snapshots of a live system, how can I best avoid problems due to the snapshot being taken during things like upgrades? Presumably this wouldn't be catastrophic, since it would be less serious than a power outage during the upgrade, but it could cause at least some amount of inconvenience.
Don't start a backup while you are also doing an upgrade. If you are doing both via a cron script, then have both scripts use a lock file or something to make sure they do not run at the same time, or schedule them far enough apart that the first one should be done before the second starts.