Did you ever solve this? Or can someone else shed some light on what's causing this? I'm also hitting this issue when compiling from source, I can see that for some reason opkg won't install the entire package, it always seems to omit cgi-bin and index.html without outputting any errors. I'm using extroot, space is not an issue for me.
EDIT: Ok, so obviously the problem here was the http transfer, the download was cut short without opkg saying anything and just installing what it could download.