The opening scene shows King Stephen being held in a squalid cage in Lincoln Castle. In fact, he was held prisoner in apartments in Bristol Castle, hundreds of miles from Lincoln. Though at one point he was chained, he was far too high-ranking to be caged or left in filth.
Matilda tells her son Henry (the future Henry II) that she is now Empress because "I rechristened myself this morning. One day you will be Emperor". In fact, she had legitimately acquired the title Empress nearly 30 years prior, when she married the Holy Roman Emperor Henry V in 1114 and ruled the Empire with him until his death in 1125.
Seen from the top of the church, Kingsbridge is far too large for the town it is supposed to be. The filmmakers have portrayed Kingsbridge as big as what would have been a major city of the time.
Several characters refer to Prior Phillip as a 'priest' or 'Father' and one makes Confession to him.
Philip is actually a Monk, not a priest, and only priests are permitted to hear confessions. Not monks.
Medieval people would have known this.