You certainly don't want it digging into /proc/, its contents aren't real files at all, it's a virtual filesystem which shows kernel and process statistics. It's a really bad idea to trawl it even when it's not spitting errors. /sys/ is another virtual filesystem, one unique to linux, which you should avoid trawling. I'd advise you to fix this problem on all your servers, even the ones not complaining.

What exactly are you trying to do? Are you trying to measure the size of the / filesystem alone? du -shx / should do that, the -x will prevent it from wandering into different filesystems (including virtual ones like /proc and /sys).