Is your case insert slide and slide cam adjusted properly? It's part number 97082 in the manual. If it isn't pushing the brass all the way forward when loading onto the shell plate, the brass will hit the side of the decapping/resizing die in station 1. You can see the adjustment of the travel of the cam slide on the Dillon 650 instructional manual on page 38, figure 192. It's controlled by the camming pin (part number 13371). If you raise the camming pin, the brass will be pushed all the way into the shell plate and won't hit the die on it's way up.
Also, as mentioned earlier, it sounds like you need the platform alignment tool. I had to use this tool when I got mine to get it adjusted correctly as well; without it, my brass wasn't entering the dies correctly. Call Dillon and ask for the tool.
Once I adjusted my Dillon, it stayed adjusted correctly. Someone used to have the Dillon Instructional VHS tape from the 90's on YouTube, but it got taken down due to copyright laws. Ask Dillon if they'll send you a copy of their DVD in addition to the platform alignment tool so you can see the adjustment of the slide cam and camming pin.