When at the watering hole, once Bo has successfully dumped the Hunter into the well, Mary is seen from the bust down carrying the water pot while the animals talk. Her belly is really big, much bigger than any other time. A few seconds later it cuts to the same visual again, and her belly size has shrunk.
When Felix the camel yells at the guy with the hat, it is heard as us humans would hear him, and his reins are in the wrong place. You can clearly see that none of the other camels reins are in front of him, but he's third from the road, and in that scene, he's suddenly in front of the other two, but next scene, he's back to third from the road.
When Bo and Dave see the Royal Caravan in the distance, it's more than halfway past the center of the setting sun. Next time you see it, it's backed up when Dave is yelling "Royal Caravan!" the caravan has suddenly backed up and the rear of it not even in the setting sun yet. The caravan then progresses across the horizon like normal as Bo and Dave speak, and it almost at the same point the last time it's seen as it was the first time.
There's no way a woman in labor can stay so quiet, not in a time of no pain killers. Plus, when the Wise Men come and Joseph asks "Is this your stable?" Mary also stands. Not exactly something a woman who had just given birth could do as easily as portrayed. Also, during the credits, it shows the new family travelling, presumably back to Nazareth, but they stayed in Bethlehem for 40 days before leaving during at night for Egypt after Joseph received a warning in a dream to flee.
When Abby is mistaken for a rat and corrects the dogs who interrogated her that she's a jerboa, she uses the phrase "rodent family", while people in real life use this phrase pretty often, it is actually incorrect, as not all rodents are related nor is there only one family of rodents, there are actually many families of rodents and the phrase is actually called the "rodent order" or the order "Rodentia", and there are specifically three suborders of rodents Squirrel-Like Rodents (Sciuromorpha), Mouse-Like Rodents (Myomorpha), and Cavy-Like Rodents (Caviomorpha), jerboas belong to only one of these suborders (Myomorpha).
When Bo gets Mary and Joseph to Bethlehem, he's spotted by the Miller, his old owner. The Miller ropes Bo and drags him off, not only with Mary and Joseph's bed rolls and clothes, but as Joseph said "I left the money with Bo". When the Miller drags Bo into the manger, Bo suddenly has nothing on his back, and it's never explained where where the stuff belonging to Mary and Joseph went.
When the Hunter looks into the manger where Mary and Joseph are out of sight, the goat, horse and cow can't be seen either. It looks completely empty. Bo never spoke of the Hunter or the dogs to the manger animals, but they hid? Plus when the pygmy jerboa comes in warning everyone, tho three animals don't react, as if they know they know the threat is gone, without ever being told about it.
Mary and Joseph were betrothed to each other but we're certainly not living together at the time she was pregnant. Thus they would not have been staying in the same house or sleeping beside each other as the movie portrayed.