There is normally some slop in the rods, there has to be a bit of leeway to allow for minute misalignment issues. Unless it's been run A LOT or totally without lubrication, it's actually pretty difficult to wear the holes to a degree where this would be an issue. It's far more likely that it's something else.
Another possibility, though it's also not common unless the locomotive has been abused, is the wheelset is out of quarter.