Interesting note: The 1959-60 Tony Awards was the only time that FIVE musicals were nominated: GYPSY, FIORELLO!, ONCE UPON A MATTRESS, TAKE ME ALONG, and THE SOUND OF MUSIC. Also of note, it was the only time that TWO musicals (FIORELLO! and SOUND OF MUSIC) tied for the Tony for Best Musical.
My pick for the biggest mistake in Tony history was moving the deadline for the 1967-68 Tony Awards up one month from the end of April to the end of March. This caused two worthwhile shows (HAIR and GEORGE M!) to be left off of that year's nominated list which resulted in HALLELUJAH, BABY! to be the only musical in Tony Award history to win the award after closing. The three other nominees that year were all mediocre at best: THE HAPPY TIME, ILLYA DARLING, and HOW NOW, DOW JONES. GEORGE M! and HAIR faced stiffer competition the next year with 1776 and PROMISES, PROMISES.
REDHEAD beating FLOWER DRUM SONG would be another pick.
DREAMGIRLS lost the Tony to NINE largely due to politics. If anybody wants, I'll get into the story a little deeper.
CONTACT really shouldn't have been nominated for Best Musical. It was more like a play with dancing (And no SINGING or ORCHESTRA, for goodness sakes!). If the "Special Theatrical Event" Tony was around when CONTACT played, it would have won that award instead.
BTW, Dick Latessa was a shoo-in for the Featured Actor award as Edna's dad in HAIRSPRAY.
Praying Decca Broadway will put "Don't Bother Me, I Can't Cope" on CD!