Olgar Shiverstone
Legend
The most likely mistake (and the one I used to make a lot and still make sometimes) is to design too many dead branches, creating a singular "path" through the level. As opposed to interconnecting rooms and hallways that loop around on one another. The funny thing is, this would actually be *hard* to do if you were trying, but if you're not paying a lot of attention it can happen quite easily by accident.
Imagine a dungeon level starting at A and the stairs down being at Z. If the rooms go A-B-C-D and then either H or a fork that goes to E-F-G and ends, it's still linear. There's a few more rooms to explore, but if G doesn't connect to I along with H, all you've done is create a dead branch.
This, I think is the reason that modern dungeon-based adventure design has failed -- people have forgotten that good design actually gives the PCs a fair number of choices about how to attack a particular dungeon, all of which are different paths to a goal. A lot of the 1E and BD&D adventures had this, and many of the later mega-dungeons, but lately (last few editions) it seems that the majority of WotC-designed adventures rely exclusively on linear design where the only choice is forward or back.
I find the encounter-focused design in 4E tends to encourage linear dungeon design, but it doesn't have to with a good encounter flow chart that has lots of branches.
I love dungeons, though I find for campaign purposes you have to have a lot of variety in them to keep them from getting stale. They're a great way of allowing the players a lot of freedom in approach while keeping the amount of DM prep manageable since there are still a fixed number of choices. But it does take some effort to do well.