So. Here's one for everyone. Not sure if this has been documented anywhere because I'm not sure anyone has ever tried it.
Dwip found something that's pretty nasty. I'd link to the discussion, but it took place on my blog which is, shall we say, not sanitized for language. Here's the gist though.
He's modified some aspects of the Arena. In doing so, he rewrote vast portions of the arena betting script. This new script took the existing Bethesda material and added boatloads of new stuff to it. He then took the existing Arena Spectators quest and assigned it a new script - his behemoth of a rewrite for it. What resulted from that was that some dialogue conditions in the standard arena topics are now pointing to incorrect variables.
In looking things over in tes4edit, when he copied Bethesda's script to modify it, the new script got a new table of variable indexes. Bethesda's original script skips the #2 index because the apparently deleted or modified a variable. Dwip's script did not skip this index because his was compiled fresh in that setup.
The result of course is that everything past the #1 index is pointing to the wrong variable. At least as seen in dialogue checks. I can't say for sure if this has also broken any other usage of those variables in other scripts because he wouldn't have needed to recompile any of them since the actual quest name didn't change.
Needless to say, this is a pretty big gotcha in terms of consequences. One that certainly isn't terribly obvious.
Assuming this wasn't a fluke, anyone else ever done something like that and torn their hair out wondering why everything was broken? Also seems to me that this should get documented in a more permanent manner somewhere like on the CS wiki.