This might be a supplemental first round pick, but one of the absolutely worst first round picks the Cubs made was Matt Clanton in 2002.
Granted Dave Stockstill whiffed on a lot of high picks in that draft, where he had anywhere from 4-6 high picks to draft players the caliber of Joey Votto, Brian McCann, Jon Lester, Curtis Granderson, and Jonathan Broxton and whiffed on all of them. (That was one loaded draft, and the Cubs blew a ton of high picks that year.)
But of all of those blown picks, Matt Clanton was definitely the most unconscionable. He was only regarded as a 3rd-4th round talent by most to begin with and had such a bad attitude that he got kicked off his JUCO team right before the draft. Yet Stockstill picked him ahead of what was a really loaded 2nd round that year, and Clanton wound up pitching a grand total of 4 IP in the minors.