Greetings:

I just bought 4 new wheels and tires for my 2002 S2K and find that one wheel doesn't fit on to the hub because the hole is about 1/4 inch too small. The wheel has Honda stamped inside and looks just like the others that fit. the hub takes any of the other wheels so it's got to be the wheel!

Wheel and Tire information:
Wheel numbers on inside rim Spokes --Honda 15X. S2A67SC. 16 X 7

 

It sounds to me like you are trying to put a rear AP1 wheel on the front, not supposed to fit. You do know that your car came with staggered wheels with different widths, offsets, and hub bores front/rear?
For reference, the OEM MY00-03 (AP1) wheel sizes and offsets are as follows:

Front: 70mm hub bore
16" x 6.5", +55 offset, 205 tire

Rear: 64mm hub bore
16" x 7.5", +65 offset, 225 tire (a really WIDE treadwidth 225)

The wheels are set up this way so that in case of a flat rear tire, you move a front wheel to the rear and run the donut on the front.
Under no circunstances should you attempt to run the donut on the rear.

Hub bore thread (with pics)

 

Or they are for an Accord or something. They are not going to fit unless you drill out the center bore on the wheel. I actually would not recommend to do that though because you will lower the load capacity of the wheel.