touching the bottom of the hole. What feels like "bottoming them out" is probably hitting imperfect threads. You can test this by hand tightening, then using a wrench. You'll see that you can turn it some more with the wrench, which means the stud was not at the bottom of the hole yet. ... But op is right either way. Hitting imperfect threads or hitting bottom could cause the stud to sit a little crooked.