I am not quite sure what you are refering to. I set in options so it won't add anything to the hotbar automatically, other then skills and it works as advertised.
Try this with a spellcaster:
1) Take your cantrips, domain spells if you have them, level 1 class abilities, and any other 'always memorised' or 'always prepared' spells off your bar.
2) Save your game (Remember this point: saving with your bars blank)
3) Go to prepare your spells and change your prepared spells - unmemorise one spell.
-> The game will immeidately fill your bar up will ALL of the cantrips, always-memorised spells and class abilities you just pulled off, dumping them into the nearest available slots.
-> There is NO way to tell the game NOT to do this, and NO way to PREVENT it doing this.
-> It will do this ANY time and EVERY time you interract with your hot bars in any way, and nothing you can do about it.
4) Pull all the unwanted things back off the bar.
5) Now memorise another spell.
-> Pop, they're all back again. Can't stop it.
6) Load your save game, that game that you saved with your bars set up in a specific way that did not include those cantrips and class abilities.
-> Pop, they're all there, cluttering up your bar as soon as the game loads in.
