It is possible to have insufficient adhesive and the solder tension from the wave washed the parts away.  Do the glue dots have a mounded or flat appearance?  How are you dispensing the adhesive?  What component packages are you seeing this with (1 type, various types, etc).  What type of wave machine do you use?  Is it a flat wave or angled?  Do you have a chip wave also operating at this time?  What is the speed of the conveyor?  What is the wave depth?

Kathy