The weld metal is usually always much harder to drill/ cut through than carbon steel.  I am sure the others will give specifics on why. The only way to avoid it would probably drill them right the first time or spend some some extra money on an awesome drill bit.  The metal around the HAZ has a different chemical composition than the non affected zone.  Just wait....these guys will give a much better answer than mine. 

Hello PA, a number of factors can have the effect that you ran into on your hole re-drilling. Type or grade of material will determine whether the welds will become hard in many cases. Whether pre-heat and post-heat were used can have an effect depending on material grade. If you plugged the holes without cleaning out or off the machining, drilling, or tapping fluid or oil, could possibly contribute to the hardness of the weld filler metal because the carbon-based fluids could combine with the weld metal to add to hardness. Type of welding process used for the plugging could contribute, sometimes dualshield FCAW weld deposits will exhibit less finished hardness than the same weld performed with GMAW, similar types of conditions can be noticed depending on the type of SMAW electrode that may have been used. Quenching or rapid cooling of welds after completion can have an effect and should be taken into consideration.
     In general, if you are going to plug holes that will need to be re-drilled and/or tapped, try to clean the old holes of any sorts of cutting, drilling, or tapping fluids. Use a bit of pre-heat and post/heat while filling these holes and allow them to cool slowly after the welding has been done. When possible try to use a welding process and filler or alloy selection that remains ductile after the welding has been done, various alloys and such will exhibit different as-welded hardnesses. There are certainly other contributing factors and the others who have already responded and will soon respond will have additional thoughts for your consideration. Best regards, aevald