How to fix a door that closes, but is still too close to the frame, causing the hinge to pull out
The problem with the hinge pulling out is caused by the mortise being too deep either on the door or frame.  Look at both sides of the hinge and determine if one or both are recessed below the surface of the wood stock.  Remove the offending side of the hinge and shim it out flush to the wood surface with some solid cardboard cut to fit the mortise. Reinstall the hinge over the shim. This should allow the hinge to close completely without putting pressure on the hinge screws.  

As far as warping is concerned, that is not normal. Would have to see a pic or have a better description of the problem in order to address it. You mentioned cutting .25 inch off a side. How did you do that?  If not cut perfectly straight, that may be a factor in your hinge problem.