I bought a lower from a company well-loved on this forum, and just "knew" there wouldn't be any fitment problems with my Colt 604 upper, which I've used on several other lowers with no problems. However, after completely assembling the thing, I found out that the upper and lower wouldn't fit together unless forced closed, and even then the take down pin would only go in half way. It was pretty disappointing, but I always try to learn from such things.
My new methodology for AR lowers is to test-pin the upper and lower together, before anything else is done. I've been tempted to take the upper along with me when purchasing a lower, to try the fit before buying, but I doubt that the seller would appreciate that.