I find them somewhat difficult to put back in as well. I put the bottom in first, then find the side spring clips and squeeze them and pop them in (both sides at the same time), then same with the top spring clips.
I do find the frame of the screen flexes quite a bit when putting it back in but once in, it flushes up fine with the window frame.
Regarding cracking the frame, are you sure it's not just the factory seam where the two ends of the aluminum frame butt together? If you look closely at your other frames, you will probably see a joint that shows up more while the frame is flexing (at least that's the case with my screens).