I have made these trousers once and had no issue. The pieces look as though one side has been trimmed already doesn’t it?
What I do I rest the two edges together and pretend the side that looks trimmed is pointy like the other piece and then I align the top and side edges up, not worrying about the corner and stick a pin in to hold them together. Then I pin from there down to the cuff but only after I do the same to the cuff edge – basically I pin both ends and fill in the gap with pinning but I pin from the top.
If you align the top, pretending the bit that looks clipped doesn’t look that way, you shouldn’t have any problems. It actually becomes hidden in the seam allowance so won’t bother you when you go to sew the crotch seam itself.
This isn’t the only pants pattern to have this “feature” and in time it will seem less annoying. You can find ways to work around it and see the benefits of it in time I’m sure.
I have sewn pants as per the instructions (sewing the in seam and then the crotch) and also using other methods (sewing fronts and then back crotch seams and then the inseams) and each time it hasn’t been a problem.
It might have something to do with reducing bulk at the crotch when you sew that seam so don’t worry just be sure to align the top and sides of the crotch and leg parts of the piece you are sewing and you should be fine.
I hope that makes sense.
