Save the rule as a manual rule first, then open it and read the list of players SaberSim put in it.
A manual rule is a snapshot. It shows exactly which players matched your logic at the moment you saved it, one group at a time. Use the Auto/Manual split button on the save to choose manual.
Then expand the rule and read each group. If the rule says "no more than one QB or RB from the same team," you should see one group per team with that team's QBs and RBs in it. If a conditional rule pairs defenses with running backs, you should see one group per defense with the right team's running back in the secondary spot.
Two things tell you the logic is off before you build. (1) The player list doesn't match what you meant, or (2) the save button says it will create zero manual rules, which means nothing qualified, usually because a position box isn't checked.
Reading the groups also shows you where to refine. If a defense rule is pairing with a backup running back you'd never play, add a stat requirement so only backs over a projection threshold qualify, save as manual again, and check the list.
Once it matches, edit the rule and save it as an auto rule so it recalculates from the latest projections every time you build.
Related: Why aren't my lineup rules working?