When Basanio and his entourage are walking with Portia to inspect the chests they pass a pond with a black swan. Black swans are from Australia and weren't known to Europe until after their discovery in western Australia by Dutch explorers in 1697. The Merchant of Venice takes place more than 100 years earlier.
When Portia and Nerissa arrive disguised as s judge and a clerk they have a letter with them. When the duke reads this letter out loud it can be clearly seen that there is also text written on the back of the letter. The duke, however, finishes reading the letter without turning the letter around.
Approximately 0:02:50 into the film, camera equipment and a man with a black baseball cap w/white logo are seen on the left hand side of the frame. It's a very quick cutaway scene after a couple shots of the white balcony.
When the Jews are carrying the Torah around the synagogue, the prayers and garb is appropriate. The Torah would only be taken out to be read. Traditional Jews only read Torah in the morning, when the light for reading would be best before the advent of artificial lighting. Therefore the Torah would not have been out at that time of day.
In a couple of occasions the name "Mexico" comes up. While Mexico was officially called "New Spain" while it was under Spanish rule (such as the time the movie is set in) in practice "New Spain" and "Mexico" were used interchangeably (hence why the colony directly north of New Spain was called New Mexico, for example).