Most likely this is being cause by no escape route for the flux gas when the PCB enters the wave. If the clinch is too tight or there is no escape path the flux gas will escape out the bottomside barrel when the unit exits the wave.

A tight clinch will pull the LED tight/flush to the board surface and not allow for the gas to escape leaving what looks like a blow hole.

I hope this helps.

It is possible that if the clinch is too tight then the LED will form/sit over the top of the hole not allowing the hot gasses to escape from the flux and other items during wave soldering. Loosening the clinch a little may help in allowing the gasses to escape from the top of the joint.

Sounds to me that the tight clinch is acting as a dam preventing the flow of both the flux and the solder thru the vias. When you relax the clinch the materials flow smoothly eliminating the blow holes.