That's very-likely the case. Even a decent majority of commercially sold epubs will match sigil's former structural requirements. It's just that you can longer rely on ALL epubs matching that structure (especially if they originate elsewhere) because Sigil no longer forces epubs into any kind structural "standard" when first opened any more.

I leave the "Show Full Paths in Book Browser" preference setting on at all times, so that I always know for sure what the structure of any particular epub is.