Leonel wasn't infuriated because there was a second Shadow Sovereign. From the very beginning, he had been aware that there was more than one. In fact, he knew a second one in Mordred.
When he first learned about Shadow Sovereigns from Uncle Montez, he had introduced it in a way that Leonel knew from then that there would always be more than one.
Without a doubt, the true reason Leonel was pissed was because Little Blackstar had been hurt. It wasn't a devastating injury, but it was definitely one the little mink would need some time to recover from.
Leonel had always treated Little Blackstar like a little brother, a child that was still growing up. This was why he rarely if ever used Little Blackstar in battle even if the little one was a powerful warrior. Leonel had no doubt that compared to these geniuses of the Void Palace, Little Blackstar was no worse. However, he was still reluctant to truly let him loose.