In "Goodbye, Old Paint", the episode where that painter Dubov doesn't want to show them where he hid the transmitter, and Mr. Howell keeps coming up with schemes to try and trick him into using it, why at the end is Mr. Howell and the Skipper making Gilligan paint the hut? It looks like as punishment, but for what?
Gilligan didn't really do anything wrong in that episode. Mr. Howell is the one who should have actually been up there painting, since it was his schemes that backfired.

That said *whew*;) , are there any other episodes where Gilligan didn't do anything wrong but is punished anyway?

Smile your On Mars Camera.

Gilligan was the kooko at the end, it was his fault he broke the lens, but they all didn't really need to chase him into the feathers.

Here's a link to a thread that I started awhile back that shows some more examples:

http://www.sitcomsonline.com/boards/showthread.php?t=147130