There are a few possible issues here.
1) The pump was made wrong, or rebuilt wrong, with the hub pressed into the wrong spot.
Check the amount of shaft lead sticking out from the hub and compare it against the old pump that fit....if you still have the old pump.
Check both the shaft lead and the hub location because the shaft itself may be made wrong (too long or not pressed in far enough on the bearing)
2) There were two pump styles, standard and heavy duty. The HD pump uses a larger diameter shaft and a large diameter and thickness hub. Usually the HD parts will not interchange with the standard duty parts (pulley bolt spacing and center hole and fan clutch hole and bolt spacing).....Buuuuuut, if this is a rebuilt pump I can envision any number of Effups being put together in todays sad state of aftermarket parts.
Measure the pump parts to be certain they match what you need.
The rest of the pump measurements, housing, bolt locations, mounting pads, water pipe locations and so on should be the same.
If this is an aftermarket pump then you must get to checking all the measurements.....who knows, maybe they built the pump you have with extra thick pump to block mounting surfaces causing it to stand off too much.
Last, do some double, triple, quadruple confirmations about the parts you have and the parts you are supposed to have. The auto parts store computers are often VERY wrong with the information they have about what is the right part to use.....That is not the counter persons fault, but the fault of those verifying what is entered into the comuter.
Good luck, and let us know what you come up with.