Solo cups are fine for clones but not plants.

Intersex traits are 100% genetic that can be induced by environmental conditions. The environment doesn’t cause the traits, they were always there.

The seeds may have recessive or dominant intersex traits. There are no guarantees either way. If it’s in the mom, it’s in the babies. That being said, it doesn’t mean you can’t find something stable enough in the seeds to grow without seeing intersex traits. Never intentionally breed with any of those seeds in the future though.

What is the light schedule and what are you growing, autoflowers or photoperiods?

Intersex traits are passed on to seed progeny as dominant or recessive. The only way to know is to stress test.