These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Incest Subtext: The Duke of Anjou kisses Mary of Guise on the lips for several seconds. She is his aunt. He is also seen holding her naked body.
On the other hand - they're French. And the death scene is very much played for drama, her nudity implies Walshingham murdered her while they were in bed together, and her nephew covers her body.
Magnificent Bastard: Francis Walsingham. Tortures Catholic priests, cuts the throats of boys sent to assassinate him, murders female pretenders to the throne, but still comes up smelling more or less of roses. And by the end of the film, under his tutelage, Elizabeth herself.
Narm: So much in the sequel. Example would be the part where Bess spins in place for no reason at the end of the battle against the Spanish Armada.
An intentional example:
Sir Walter Ralegh: Potatoes. You eat it. Very... nourishing. Tobacco. You breathe its smoke. Very... stimulating.
Paranoia Fuel: YMMV. The dress that was given to Elizabeth as a gift, that her hand-maid wore when she went to meet with Dudley. It turned out to be laced with poison. The contrast of her crying in pleasure to screaming in agony as the poison first began to itch and then kill her was a creepy one. That she could do nothing but whimper and die... and her body afterward. *shudder* You are left to wonder did she scratch herself till she bled, or was that the poison itself that cause her skin to blister and burst? Either way, it gives one pause when receiving clothes.
Unfortunate Implications: Lets just say both films (especially the sequel) take a rather dim view of the Spanish and Catholicism in general.