First fortress: Not realising wells don't block pressure. Only realised this when my high pressure well on Z -20 (fed by the Z 0 river) had flooded the lower half of my fortress.
First fortress with magma: Not understanding magma pressure due to an ambiguous entry on the wiki. Flooded the booze storage with magma before I managed to wall the area off. Tantrum spiral ensued (No water yet, was looking for the aquifer). I made the wiki a little clearer on this point and reclaimed.
Now you should know that my HP Elitebook 8530w has a hardware issue with the touchpad.
1. You cannot disable the touchpad.
2. When you hover your finger for a while above the touchpad it will register a click (after about 5 min). Since I keep my hands on my keyboard at all times while playing DF2 it will sometimes generate such false clicks because the knuckle of my left thumb is constantly hovering partially above the touchpad.
In the second fortress I mentioned, which I reclaimed, a rogue click while designating mining designated exactly the single tile between the previously magma flooded part and the workshops. I was really glad I built the still in a room with a basalt door for no good reason. It was the only part that flooded.
Then I dug into HFS. I had set up an elaborate trap corridor with legendary military dwarves at the end. Alas the demons pathing realised it was faster to just fly straight up trough the magma pipe into the volcano crater and murder my non-military dwarves from behind.
Also I once embarked on a plain with a continuous aquifer on z-level -3. I build the entire fortress out of wood aboveground. Only while typing this I realised that it is possible to dig trough an aquifer with only two z-levels of soil above it.
The fort was pretty nice though. I only had constant war with the elves. (Wooden fortress)
Pictures made with Overseer. (The crenellations and stairs are rotated 90 degrees, due to a wrong export from blender to .obj. (.obj has Y as the vertical axis and blender has Z, thus 90 degree rotation).