I was also looking at my PCB design, and I put traces and a via under each LED(and the silk screen goes over the via making even higher).
Several things to watch out for:
1/ Avoid placing any silk screen under a component, especially on any copper (tracks/vias/pads) as it can lead to poor solder joints.
2/ Avoid placing vias within a pad as this allows the solder to flow down the via, thereby leaving insufficient solder on the pad itself. This can lead to dry joints & components that easily lift off the board. Where the design has no alternative (ie mosfet heatsinking to the other side of the board), consider using a thicker solder paste stencil (ie 0.2mm) so that you lay down more solder, or consider plating the vias shut, or having their holes filled by the board manufacturer.
I moved the vias and traces for future prints, but sadly I'm stuck with these for the short term.
There are a few design procedures that can help:
1/ Try & have the tracks leave the component pads from the back of the pads (ie leading away from the centre of the component).
2/ Try & place the exiting tracks "symmetrically" from all component pads.
3/ If really critical, close up the
width of the pad to be very close to the width of the pad itself. This aids in "self alignment" when the solder is molten. Make up for the reduced pad width by adding to its length to ensure adequate paste is layed down.
IconicPCB is quite correct. It is critical to preheat the solder paste to ensure the flux is not trapped under the surface when the melting point is later reached. Any trapped flux can lead to nasty "balling" which is what you are experiencing.
A Google search should lead you to the paste manufacturer's specifications.
I hope this helps.