For me, it's glowing stone like microcline, orthroclase, and realgar. Everything goes from a nice grey or brown to a OH GOD IT'S YELLOW.
Doesn't mess up the layout, per se, but messes up the look.
But you can lay floor over mined rock surfaces, can't you? And I know you can, if necessary, remove walls and rebuild with another color stone.
In fact, one of the neat things about Dwarf Fortress is how fluid your fortress really can be. If you need to dig a moat, but your farms are there, just build a farm somewhere else and put walls as necessary to contain the moat. In fact, I just had a similar problem, so I made a short dog-leg in a distant corridor to avoid a new moat (and if I'd really wanted a nice, straight corridor, I could easily have redone the whole thing).
Chasm, river, Adamantine, Magma... Anything underground, really.
Why is it that it always happens right in the biggest and most time-consuming-to-build part of the fort?
OK, I happen to think this would be great! Not a disadvantage at all. I love working my fort into the existing world. If I didn't have to do that, all my forts would look alike. And let's face it, there are worse things than discovering a convenient source of magma - or a chasm or underground river - right off the bat! An inconvenient aquifer might be a pain, but the rest of these?
#3 is using a bad design. 1-wide hallways don't cut it, and the beds need to be further away.... the basics you don't learn until you've had a couple kings show up. also, not leaving enough room for traps, or whatever else is vital to survive.
Again, the game is fluid enough to overcome a lot of these problems. I've widened corridors before. Yes, I lose some space from the rooms alongside (unless I want to move everything a space), but it's certainly possible. And it's not all that impractical, either, since I always seem to have tons of dwarves who are unnecessary for serious work.
Admittedly, I'm still a newbie at this. And although I planned out my first fortress, I'm taking a more casual approach with this one. That will probably come back to bite me in the ass, but without knowing where in the world the magma pipe or underground rivers lie... well, it's hard to plan out everything.
But I like unexpected discoveries. And I keep learning just how flexible Dwarf Fortress can be. If I really want to do something, I can usually do it - no matter if I'd already dug or built in the area or not.
Don't you think?
Bill