As noted elsewhere, many of the issues along these lines appear to occur with EPUBs that have been created by the users as opposed to those available commercially.
The problem may be in the resulting size or the method of conversion. That said however, although we have the standards for EPUB widely available, the end-user tools that we have to make the conversion still appear to be in its infancy. (The standard tool available, Sigil is version 0.5x)
I wonder therefore, whether the issue (bug) is with the quality of EPUB files and the tools we use to make the conversion?