The original version of Shirobako which aired on TV was pulled off streaming sites like CrunchyRoll due to rights issues (see ANN for more info). Since then, an edited version has been added to replace the original. What were the issues, and what changes were made to the episode?
I've watched the original (now pulled) and the edited version (currently on CrunchyRoll). The only change I noticed was with regards to the dialogue in the play which Shizuka attends, about 11 minutes into the episode. The original dialogue was clearly taken from Samuel Beckett's famous play Waiting for Godot. This play is still copyrighted. To make things worse, as is described in the Wikipedia article linked, Beckett was strongly opposed to having female actors cast in the play, which the episode has. While the amount of the original it used was quite small (there's only about 15 seconds of dialogue), Japanese copyright law has no fair use policy, and so this could still be an issue.
The modified version only changed the dialogue during the play. Rather than taking lines from the original, the new dialogue is a noticeable reference to Waiting for Godot, but not taken directly from the play. The animation did not seem to have been modified, so the characters' lips didn't exactly match the new dialogue; this will likely be fixed in the final DVD version.
The references to Space Runaway Ideon seem to be unchanged. Both the original and new version called it "Idepon". While many initially suspected that these were the source of trouble, the Godot references seem to have been the bigger problem.