Short Answer:
After 1520, the lands in the Americas were certainly under the Castilian crown.
Long Answer:
As far as I know the lands in the new world were all under the crown of Castile and had no connection with the crown of Aragon., except that Ferdinand and Isabella may have jointly ruled them from 1492 to 1504, and when Queen Isabella of Castile, etc., died in 1504, her husband King Ferdinand of Aragon, etc., became regent for their daughter Queen Juana of Castile, etc.
The new lands across the sea discovered in 1492 and later were originally ruled by Castile, I think, since the ships that sailed to them sailed from ports in the Castilian group of kingdoms.
In 1492, the titles of Ferdinand and Isabella were:
Don Fernando e donna Ysabel por la gracia de Dios rey e reyna de Castilla de Leon de Aragon de Cecilia de Granada de Toledo de Valençia de Galizia de Mallorcas de Sevilla de Cerdena de Cordova de Corçega de Murçia de Jahen de los Algarbes de Algesira de Gibraltar e de las Yslas de Canaria, conde y condesa de Varçelona y sennores de Vizcaya y de Molina duques de Atenas y de Neopatria condes de Ruysellon y de Cerdania marqueses de Oristan y de Goçiano
They did not change their titles when the Americans were discovered but continued to use the same set of titles until Queen Isabella died in 1504.
Isabella's daughter Juana la Loca became queen of Castile, etc., in 1504 and used the title:
dona juana por la gracia de dios reyna de castilla de leon de granada de toledo de galicia de sevilla de cerdena de murcia de jahen de los algarbes de algeciras de gibraltar e de las islas de canaria, señora de vizcaya e de molina princesa de aragon archiduquesa de austria duquesa de borgoña
In 1504, King Ferdinand of Aragon changed his title to:
Nos Ferdinandus Dei gratia Rex Aragonum, Siciliæ, citra et ultra Farum, Jerusalem, Valentiæ, Majoricarum, Sardiniæ, Corsicæ, Comes Barchinonæ, Dominus Indiorum maris Oceani, Dux Athenarum et Neopatriæ, Comes Roxilionis et Ceritaniæ, Marchio Oristani et Goccani, administrator et gobernator regnorum Castellæ, Legionis, Granatæ etc. pro Serenissim a Regina Johanna, filia nostra carissima
In this, he added the title:
Dominus Indiorum maris Oceani,
That translates as:
Lord of the Indias of the Ocean sea;
Thus Ferdinand added a title indicating rule over the new lands.
Ferdinand stopped using that title in 1506, and his daughter Queen Juana and her husband King Philip I added the Indias to their titles.
Don Felipe e dona Joana, por la gracia de Dios, rey e reyna de Castilla, de Leon, de Granada, de Toledo, de Galizia, de Sevilla, de Cordoba, de Murçia, de Jahen, de los Algarbes, de Algezira, de Gibraltar e de las Yslas de Canaria y de las Yndias, Yslas y Tierra Firme del Mar Oçeano, principes de Aragon e de las Dos Seçilias, de Jerusalem, archiduques de Austria, duques de Borgoña e de Brabante etc., condes de Flandes e de Tirol, etc., señores de Bizcaya e de Molina etc.
So they added the title of King and Queen of "las Yndias, Yslas y Tierra Firme del Mar Oçeano" or of "the Indias, the Islands & Mainland of the Ocean sea" to their title.
By the Treaty of Villafáfila, King Ferdinand II renounced in favour of his daughter, Queen Joan I of Castile, his rights in America (June 1506).
http://eurulers.altervista.org/aragon.html2
The Treaty of Villafáfila is a treaty signed by Ferdinand the Catholic in Villafáfila on 27 June 1506 and by Philip the Handsome in Benavente, Zamora, on 28 June.
The treaty recognised the incapacity of Ferdinand's daughter and Philip's wife, Joanna the Mad, to reign on her own as Queen of Castile. Joanna had succeeded her mother, Isabella the Catholic, who had appointed her husband and co-ruler Ferdinand as regent of Castile in the name of their mentally unstable daughter. However, Philip demanded his share in the government. The Treaty of Villafáfila followed the Treaty of Salamanca (24 November 1505), in which Ferdinand and Philip were recognised as co-regents in Joanna's name. However, the new treaty required Ferdinand to cede all power to Philip and retire to his own hereditary realms, the Crown of Aragon, to which Joanna was also heir presumptive, and proclaimed Philip jure uxoris King of Castile. Ferdinand renounced not only the government of Castile, but also the lordship of the Indies, leaving a half of the income of the kingdoms of the Indies. Joanna and Philip immediately added to their titles of "Kings of Indies, Islands and Mainland of the Ocean Sea".1
The treaty was made moot very soon, since King Philip I died on 25 September. This left Ferdinand free to assume the government of Castile, and again return to the regency of the crown and recover the title of lordship of the Indies, both of which he held until his death in 1516.1
The Indies remained in an ambiguous state from the death of Philip in 1506 to the death of Ferdinand in 1516, being half a personal property of the kings (a "lordship" with absolute power for its lord), and half a kingdom of the Crown (ruled under the laws of the Crown of Castile).1 From 1516 to 1520 the Indies were extraofficially part of the Crown of Castile.2 In July 9, 1520 Charles V, Holy Roman Emperor incorporated them explicitly into the Crown of Castile and he forbid any future separation.2
https://en.wikipedia.org/wiki/Treaty_of_Villaf%C3%A1fila3
So apparently King Ferdinand II of Aragon, etc., was (possibly) a co ruler of the Indies with his wife Queen Isabella from 1492-1504, and ruled them from 1504 to 1506, then ceded them to his daughter Juana and her husband Philip I on 27 June 1506, then regained control of Castile and the Indias after Philip died on 25 September 1506.
From 1516 to 1520 the lands in the Americas were under unofficial Castilian control, and that control was made official in 1520.
Since Simon Bolivar lived from 1783 to 1830, if the scene in the television series was set after Bolivar was born it would have been at least 263 years after 1520 and at least 277 years after 1506. Therefore, I see little reason to suspect that the legal weights and measures in Caracas would be specifically Aragonese in 1783 or later.
Therefore, I agree with the suggestion of Carlos Martin that possibly the inspector said that the weight was wrong because the shipment was being sent to someplace in the group of kingdoms and lands ruled by Aragon instead of to someplace in Castile.
