I’ve used a lot of 12x3mm and smaller magnets without them jumping up and attaching to the print head but I did have it happen with larger 40x10x3 rectangular magnets. It ruined the print and caused a huge clog, but I came up with another way to embed magnets because of it.

I designed a long 10x3 tunnel into the print, printed the object without pause, then slid the magnets into the tunnel. I printed a couple spacers to go between the magnets to place them how I wanted them and I printed a plug to glue into the opening of the tunnel. The plug was a second color so it stood out and made a little accent.

I haven’t done it yet but I thought it would be cool to add a little decorative design to the original object to be printed in a second color and make the tunnel plug the same second color and hide it in the decorative design.