That usually happens when a s3pack lot contains a bunch of third party CC. Typically, I use Custard to remove all the extra content, save the sims3pack with only the lot in it, and then extract to package using S3Pack Extractor.
It's an extra step but it gets rid of all the extra files and ensures that I don't get a bunch of CC that I don't actually want.
And because apart from slogging through all those package files that extracted with the lot in S3PE, I never found a way to identify the lot package itself from the other CC
