Here's another issue we see from time to time involving the old, familiar, 0.1" pitch headers. When initially laying out the board, the footprint for the break-away header is used. It's small and easy to use. The headers are cheap and easy and you don't need to stock a bunch of different pin-counts.
That's all fine and dandy until the next rev of the prototype when you decide to change to a shrouded header for the additional reliability and pin protection afforded by it. When making that change, don't forget that the footprint with the shroud may very well be bigger than the break-away footprint.
Get out of my cap's space, man