You were not 
The onion skins show the presence of paint on a layer so a ‘flood filled’ layer will always be full of the onion skin colour.
You’re supposd to do any artwork of a transparent layer.
If you want a particular fixed background colour, you can put a layer underneath and flood fill it with the colour or your choice, or paint some kind of background scene on it.
All animated ‘characters’ should be painted on a transparent layer and different characters should be painted on different layers to give ease of future development and editing, especially erasing.
It seems that my initial suspicion was correct.