Why was it an issue?

The loyalty of the remaining Muslims and Moriscos

Also many Christians in Spain doubted the loyalty of the remaining Muslims and Moriscos. During the 16th century this distrust increased due to several rebellions and, above all, because proof emerged that some Moriscos living on the coast were giving support and assistance to Ottoman and Barbary ships. This provoked fiery speeches against them which were full of arguments justifying discrimination or, even, their elimination.

There is also a great convenience in punishing them with fines and special taxes to make them poor, because it is very necessary for their spiritual and temporal advantage. Their property is good for nothing but to impoverish the Old Christians and, above all, we know that if they could go to Algiers or damage us in Spain, the money they have would buy weapons against Christians

Letter from Archbishop Ribera, c. 1590

In a few years they [Moriscos] will have multiplied so that they will exceed old Christians in number of people and in quantity of finance, especially gold and silver, because they have collected everything and spent nothing

Martín de Salvatierra, Bishop of Segorbe, 1587

Now, I want to propose some remedies to discuss in this meeting The first one is that the Inquisition proceed against all the Moors from the Kingdom of Castile without sparing their lifes or giving them a natural death or permanent exile or perpetual galleys [And to restrain the multiplication of the Moors] we must take their sons and daughters away from them

Query submitted to the State Council by the Marquis of Almazan, 1590