Is this lead free solder or tin/lead? In lead free it seems that blow holes or surface voiding is more common. This is due to the surface tension of the alloy as well as interaction with the flux. In general lead free solder needs a more aggressive higher solids content flux than tin lead to get the same results. Temperature of the board may be another issue as well as dwell time in the wave.

Another contributing factor is the board surface finish. If it is plated with gold, silver or tin there could be organics or salts from the plating bath trapped in the plating. This would not show up in a cross section. When the solder fills the barrel the organics or salts will erupt and blow the solder out. This also occurs sometimes on SMT double sided boards where the first side to be assembled will form blow holes after the component is on it and it is reflowed a second time.

Check you plating, check your flux to make sure it is compatible with lead free if you are soldering with lead free. Also run a longer dwell if it is lead free try 5 seconds.

If you are soldering with tin/lead check the plating this can be tested with SEM to look for inclusions in the plated finish.

Blowholes are caused by outgassing of flux, mositure or other organics in the PTH. So I don't understand your statement that there was no indication of voids but you could see where the blowhole was forming.

A void will form first and if there is enough outgassing and pressure it will become a blowhole. If there is no indication of a breach in the wall of the PTH (they are very hard to find sometimes) then the problem could be trapped flux or organics in the PTH.

The through hole component could be capping the top of the PTH and this would trap the flux and cause a blowhole. If the problem is moisture in the board and you missed the breach in the PTH then baking the boards in a oven at 150 C for 8 hours should care that issue.

The most common causes of blowholes is expansion of a liquid or gas at high temperatures escaping through the solder, leaving behind a hole. It sounds as if you looking for one of the more common causes for blowholes, which is material escaping from within the PCB layers, through the plating and into the molten solder.

Sometimes these cracks or holes in the plating can be hard to find, if they are not viewed in a single cross section, that doesn't necessarily rule them out. Does transmission X-ray of these PTHs show any disjointed Are the boards going through any sort of washing (solvent or DI) process prior to the wave soldering process? If so if these are not completely dried, liquids can be trapped within the PTHs and lead to blowholes.

Another cause can be a water based flux that isn't completely dried/evaporated can expand and cause the same effect.