It might be that your digestion of your Insert is not working out you have blunt ends. So it will just ligated several inserts. But i am not sure. And i hope you are not using BL21 for plasmid replication. Not recA mutation. But BLR have it or other K 12 strains. And are sure that you are not cutting into your plasmid?
No, of course if you use more magnetic beats you will increase you yield depending on your experiment design. But as I said you beads have capacity ana useing a lot of beats are not recommend. But in different concentration as you said,