By default, and only option, Stogram updates all users at once on startup. This puts a large load on Instagram servers which results in some requests being denied or timing out - which results in corrupted files from incomplete downloads. As it is, Stogram doesn't know these files are corrupted, and makes no attempt to redownload any files - once a post has been downloaded, its not downloaded again.
This issue can be easily fixed by not having Stogram update automatically on startup, update users one at a time, or limit the number of active downloads.