You can trim them down with a grinder or file, clean up the threads with a special "knife edge" file.

Or you can counterbore the pilot holes so the shorter screws work.

There are electricians pliers that come with a shear for trimming machine screws.

http://www.homedepot.com/p/Klein-Tools-Multipurpose-Electrician-s-Tool-1001/100647872?cm_mmc=Shopping|THD|G|0|G-VF-PLA-D27E-Electrical|&gclid=CNnVtJudkcwCFYomhgodevQL4g&gclsrc=aw.ds

Agree with Sombreuil -- Just installed some last week and used electrician's pliers to shear them off. How far the threads extend into the knob varies by knob/pull type so you might need some trial and error. Here's just one example of the tool you can use. If you look just past the pivot point toward the handle, you'll see a number of different size threads where you insert the machine screw and cut it off to length. Be sure to insert the screw from the threaded side, not thru the back side (DAMHIKT)Stanley version

IF you cut or grind off, put a nut on first, pat the cut and when you remove the nut, it will straighten out the threads.

One and one quarter inch long pan head 8-32 machine screws

Do what I do ... take the knob and the door to the hardware section and try sizes.