If it is a standard J Bass pick guard maybe you have 2 bridge PUP's which are 94mm wide or thereabouts and hence why one won't fit in the pre cut opening that probably measures about 91mm wide.

If this is the case you have a couple of options:

1. Source a smaller Neck PUP - I have both spares no longer wanted but their sound is only average with fairly low output hence why they were upgraded
2. Gently sand and file out the inside of the pickguard until the PUP fits. I have done this a few times in the past and it is a very, very slow and painful job