Ender 3 home location
The Z stop can be loosened and moved up but it seems weird that it would need to be moved and I don't think that would fix your issue. The Z height should be the same for the auto home and printing. I auto home then disable steppers and slowly move to all 4 corners. I have caught myself resting my arm on the X axis and moving it down. If that happens I manually move the Z until it just barely presses the Z stop in when I hear the button click. I have heard some say that they got a warped bed. I wonder if that's the issue. A glass plate would be a good way to be sure or maybe using a straight edge to check.You could also double check the tightness on the wheels is just right. Tomb of 3D Printed Horrors has a really good setup video called "Creality Ender 3 assembly and pro build tips" that has a few other tips that really helped me get set up well.