I agree that you both shouldn't have the same FRN so you should get it fixed. But you're right that it's been a long time--it goes back to your original KC8 calls that were cancelled in 2000. My guess that your statement "I associated my call and my wife's with the same FRN long ago" occurred when the ULS was first set up in the late 1990s (1998 or 1999). I recall you first had to register to receive the FRN, and then you found the license(s) that should be connected to that FRN (just as you said).
The fact that you've renewed your licenses since then means it's not a fatal error, but it's messy and could cause problems at some point.