Potatoes are native to the Americas. The scene in which the vegetables are kept ready for Jodha's cooking shows potatoes. The film is set in second half of 16th century when potatoes had just reached Europe and potatoes were introduced in India much later.
When Jodha comes to Agra for the first time after her marriage, a Rajput maid carries the pot of rice that is toppled by Jodha, a common custom. A closer look when the maid carries it reveals that there is a stainless steel bottom for the pot.
In the scene where Jalal goes to Amer for the first time to take back Jodha, one of the subordinates of Jodha named Madhavi, while watching him through window, comments that "Mujhe to ab bhi vishwas nahi ho raha", meaning "I still can't believe this". This is clearly being spoken in Gujrati accent. It seems unlikely that a small kingdom of Amer (In present day Rajasthan) would have hired domestic help from Gujarat.
In the scene where Maham Anga raises the issue of food-testing by the chef, she says to Akbar and the royal courts men... "Khud Jahaanpanah is baat par inkaar-e-harf nahin utha sakte," meaning "The emperor himself doesn't have the privilege/authority to raise objections on this issue." The actual phrase is "Harf-e-Inkaar." Harf meaning letter/word/point and Inkaar meaning "denial/objection." The "E" in such phrases is the Persian/Urdu style of addressing possessive forms of words. The order of the words was erroneously reversed, which changed the meaning of the sentence! Harf-e-Inkaar = Word of objection, Inkaar-e-Harf (wrong!) = Objection of word... (doesn't exist).
Young Akbar refuses to behead Raja Hemu. However, in 'TArIkh-i-Akbari' of Muhammad Arif Qandhari, (translated into English by Tanseem Ahmad, Delhi, 1993, p. 74), it is written clearly that "...The king struck Hemu with his sword and he won the title of Ghazi...".
No member of the Mughal royal family named Jodha Bai is mentioned in the official biographies of Akbar and his son Jehangir. Akbar's official biography, Akbarnama, does not mention that Akbar had any Hindu Rajput wife named 'Jodha Bai'. However, the biography of Akbar's son and future emperor, Jehangir, mentions that his mother was a Hindu Rajput princess who adopted the name 'Mariam Zamani' after marrying Akbar.