TAEB - Bugs and Limitations
It's too big. Expect about 100-200 MB of RAM usage for a fully-instantiated main dungeon, double that if it manages to instantiate Gehennom. Sometimes it uses much more for poorly understood reasons.
It's too slow. Depending on number of changed tiles, amount of monsters, etc, it can be as much as about 1 second to process input and 4 more for the default AI to decide on a move (on sorear's 2GHz P4). Admittedly, it's hard to critique bot performance much faster than that, but it does make debugging late game issues harder, and is a blocker for Interhack 3.
The mechanisms used to synchronize with NetHack are all a bit fragile and occasionally (1 in 105 level) report end of output prematurely. Not enough to motivate serious improvement efforts, but enough to produce the occasional unreproducible glitch.
Teleportitis causes item data to be incorrectly updated if it triggers during item actions (eating, pickup). Auto-recovers on sight, but still warning spam.
Group combat code is still pretty lousy in Behavioral, it has to rely on Elbereth far too often, and it doesn't even abuse it properly. Tends to die to captains and the like a lot for obvious reasons. Priorities are a little tricky near trolls, it prefers resting over dealing with the corpse, but there's no obvious safe way to fix this.
Behavioral tends to oscillate in situations where a desired action is impossible, or becomes harder to see as it gets closer; the standard example of this is a monster in a corridor, Behavioral approaches at an angle for safety, loses sight to the monster, forgets that it is there, goes back to do something else, and repeats indefinitely.