Being a novice at welding, I encountered the same thing. Before I sprayed epoxy, I would use a flash light on the backside to find those little holes and I would add another tack until they were all gone. Tedious to say the least.
I'm not sure what everyone else will say, but I wouldn't count on filling tiny holes with filler, it will just cover them leaving a chamber where rust can start. Maybe you can spray more epoxy until the holes are filled? That would be better than filler.
I may be wrong on this so stay tuned for other advice.
Good luck!
