He didn't get 'punished' by the MoM in Chamber of Secrets either, he just got a letter from Mafalda Hopkirk reminding him not to do magic out of school (and CoS comes before PoA, BTW).
In CoS, it was the Dursleys who locked him in his room and confiscated all his magical things, as a punishment for Dobby's exploding pudding ruining their dinner party (and Vernon's business deal). Up until Harry got the letter, he'd been having his best ever summer -- because the Dursleys hadn't known that Harry wasn't supposed to use magic outside of school.
And in PoA, after Harry blew up Aunt Marge and ran away, he wasn't punished either -- Fudge was very understanding about it (because of Sirius' escape), and MoM agents easily shrank her back down to size and modified the Dursleys' memories.
Fudge only turned against Harry after GoF, when he thought Dumbledore was working to depose him. And then he used disproportionate legal repercussions to try and punish/discredit Harry -- 'a trial by the full Wizengamot' -- as last seen (in Pensieve, in GoF book and movie) being used to put Death Eaters on trial for using Unforgivable Curses during Crouch's reign.
But yeah, it was kind of dumb that Cuaron put the 'Lumos under the bedcovers' in the movie, when JKR clearly states on the first page of PoA that Harry used a torch (= 'flashlight', for the Scholastic readers!) to do his homework. If he wanted to show how trapped Harry was, then putting bars (back) on his window would have done just fine.
Apart from that, though, I thought the PoA movie was a pretty good adaptation overall -- not the best (that would be CoS), but certainly much better than the low points of the series: OotP (needed more shouting, and less 'comedy') and HBP (needed more Voldemort memories, and fewer totally made-up scenes).