During the flash back scene in the court room, the younger Veronica has brown eyes, while the older one has green.
In the flashback to Lincoln's trial, the courtroom is full of people, including Michael and Veronica. However, in an earlier episode, when Veronica is given the copy of the tape by Lincoln's first attorney, he tells her that it was a closed trial.
In addition to "C-Note" and the other soldiers in the wrong branch uniform, they were also wearing the "desert battle dress uniform" or "cookie dough" pattern body armor. You may have seen it in "Black Hawk Down". It was phased out before the war in Iraq started in 2003.
In this episode, it shows that Benjamin Miles "C-Note" Franklin was discharged from the "U.S. Army". But the combat uniforms they are wearing, are only issued to the U.S. Marines. The uniform they are wearing is the MARPAT, short for "MARine Disruptive PATtern"
The name tape of Captain Meyers is on the wrong side of the uniform. It is supposed to be above the right chest pocket instead of the left.
Lincoln Burrows has been imprisoned for about a month when Michael Scoffield started planning his escape; yet on the big operation wall behind his brother's desk, the newspaper ad which helped him get married to Nika Volek has the title "Czechoslovakian Brides". Czechoslovakia only existed until the end of 1992, after which it was split into the Czech Republic and Slovakia.