Crashing:

Intersecting 3d floors: If you have the same sector heights of 2 3d floors and assign them to the same sector Legacy will crash quite merciless. So if you have Legacy instantly crash when you look into a area with 3d floors.. This is most likely the cause.

Software:

Visual Bugs:

Dancing Lines: This is a bug that's inherited from the original Doom, When walking along a linedef in Legacy it'll dance back and forth. This is due to a bug in the rendering code and it's apparent like this in almost all Doom ports that feature looking up and down. (Not in zDoom, and Hardware ports)

Hardware:

Visual Bugs:

HOM textures: Legacys translucent textures are not working in Harware mode. They are in the process of being implented. At the present they are presenting a HOM like effect, instead of translucency.

Misc:

Missing Doomguy: Not a bug per se. But Legacy have for some weird reason a limit of 1 Doomguy per map. This meaning that hacx such as used in Dystopia3 and Vrack2 don't work in Legacy.
The Hack: By placing more than 1 "player 1" starts in vanilla doom and other ports, you'll get a static doom player spawned but not controlled in the map. If you shoot at this player. You will take damadge, since you are basicly shooting yourself. This have been used to create traps and warious trigger effects in many maps. Due to this incompitability with Doom2.exe Legacy will not work right with these maps. I'm gonna try to talk Hurdler/SoM/Boris into fixing this however.