Few days ago encountered similar bug: Finder reported size of direcrory as about 300 Mb, but actual size was 9 Gb. There were no hardlinks or something like that, content inside was generated by script. This was on apfs, and size was reported instantly, so it might be bug in filesystem, not Finder.
So the problem is likely with size caching in Finder.
I tried getattrlist on my system, and ATTR_DIR_ALLOCSIZE is always 0 and ATTR_DIR_DATALENGTH is some unrelated small number (probably size of directory entry in FS, not size of its files).
When Apple converted my root filesystem to apfs, some code I wrote stopped working because on occasion (e.g., right after powering up) my code's attempt to execute a file (namely, /System/Library/ PrivateFrameworks/Apple80211.framework /Versions/Current/ Resources/airport, an ordinary executable file that certainly does exist) would fail with a "file not found" error.
