The antique desk was transported by Scottie to his home upside down on top of his SUV. However, when the secret compartment was first opened, the pen and the ink bottle were perfectly in place, and they evidently had not bounced around at all in transit or they surely would have been heard rattling around.
The goof items below may give away important plot points.
When Lizzie arrives home from Boston her father and Mr. Reagle are discussing politics right before she comes down. Mr. Reagle mentions something about General Grant taking over the Army. However, this is during Gettysburg and General Meade had just been appointed Commander at that time. Grant was after Gettysburg.