In 1562, Elizabeth nearly died of smallpox, this caused problems because she had no heir and wasn't married, which would've caused rebellions to occur and her cousin, MaryqueenofScots would've inherited the throne.
Ireland;
Elizabeth considered herself as Queen of Ireland, but they disagreed and rebelled,1559.
Taxation;
When Elizabeth I became queen, she had to pay off debt by raising taxes and to raise an army, in order to defend England.
In 1570, after the Northern plot, Elizabeth was excommunicated by the Pope and Catholics listened to him.