Well, you could actually read the dam court documents. If you put random junk into the CAPTCHA boxes sometimes you would get an error page back - over TOR - but which contained the true IP address of the server.
Where do you get this? Because the court documents in the article certainly don't say that. In fact, they seem to be saying that the IP packets themselves contained the IP:
Upon examining the individual packets of data being sent back from the website, we noticed that the headers of some of the packets reflected a certain IP address not associated with any known Tor node as the source of the packets.
That's not an error message, that's (apparently) an HTTP(S?) request being sent straight to the Tor servers. And the only way I can think of to screw up a CAPTCHA implementation to do that would be to have it construct a complete URL using the host IP instead of just using the configured host name, which would be insane.
Again: according to the FBI themselves, this wasn't "debugging data" or anything, it was packets that were for whatever reason completely outside of the Tor network.
I don't know why people seem to find it so hard to believe that the FBI would decide to target the highest-profile online illegal drug marketplace without prompting from "sinister forces"
Because we're aware of things like COINTELPRO or, for those of us in the Boston area, remember little things like Whitey Bulger? I don't trust the FBI because they've gone out of their way to prove they are not to be trusted.