In S06E09, Daenerys tells Yara that Balon Greyjoy was a terrible king. Yara responds that that’s what Daenerys and herself have in common (both of their fathers were cruel). Daenerys then says that both have been murdered by a usurper. But Aerys II was killed by Ser Jaime Lannister - How is Jaime a usurper?
The extended dialogue of the scene has no more information to offer on this in terms of context.
DAENERYS: Has the Iron Islands ever had a queen before?
YARA: No more than Westeros.
THEON: Our Uncle Euron returned home after a long absence. He murdered our father and took the Salt Throne from yara. He would have murdered us if we had stayed.
DAENERYS: Lord Tyrion tells me your father was a terrible king.
YARA: You and I have that in common.
DAENERYS: We do. And both murdered by a usurper as well.
Game of Thrones, Season 6 Episode 9, "The Battle of The Bastards"
However, if we use the books and Dany's POV chapters it makes it very clear that she doesn't think of Jaime as the Usurper but as Kingslayer, the same as most other people.
Yet sometimes Dany would picture the way it had been, so often had her brother told her the stories. The midnight flight to Dragonstone, moonlight shimmering on the ship's black sails. Her brother Rhaegar battling the Usurper in the bloody waters of the Trident and dying for the woman he loved. The sack of King's Landing by the ones Viserys called the Usurper's dogs, the lords Lannister and Stark. Princess Elia of Dorne pleading for mercy as Rhaegar's heir was ripped from her breast and murdered before her eyes. The polished skulls of the last dragons staring down sightlessly from the walls of the throne room while the Kingslayer opened Father's throat with a golden sword.
A Game of Thrones, Daenerys I
Again a later passage also refers to them by the same titles.
In the songs, the white knights of the Kingsguard were ever noble, valiant, and true, and yet King Aerys had been murdered by one of them, the handsome boy they now called the Kingslayer, and a second, Ser Barristan the Bold, had gone over to the Usurper.
A Game of Thrones, Daenerys IV
So when she says "both murdered by a usurper as well" she is meaning that the usurper killed her father due to his rebellion and his orders. She means it more metaphorically than physically.