i have. never when using my canopus ADVC-100 DV bridge, but a few times when using my dad's and my girlfriend's DV cams. (dad has a panasonic, girlfriend has a canon).
there is a solution to it..
use imovie to extract the audio.
open up the extracted audio in a sound editor, and edit it. i often find selecting the beep, then silencing it out, and pasting over with the sound from the other channel, works fine. once you're done, save the audio and go back into imovie, making sure you uncheck the original audio checkbox in the timeline.
whatever you do though, don't just select the beep and delete it, because it will result in your audio being out of sync.
while you may not be able to remove the noise completely, at the worst you'll be left with a tiny click or pop, which sounds a lot better than the annoying beep!
-Mark
(p.s. i did actually get this problem in iMovie 2 a couple of times..)