It’s important to remember how tense things already were between Aerys & Rhaegar before Harrenhall. So tense a second “dance” was about to break out.

Aerys was rightly paranoid that his son was trying to make allies of as many prominent Houses as possible in a coup to depose him. The WOIAF says Quarlton Chelsted took Rhaegar crowning Lyanna to be further proof that Rhaegar was scheming with the noble Houses.

Lord Chested was Master of Coin and later named Hand by Aerys. He was part of the Mad King’s inner circle, all lickspittles, so his views were likely just a reflection of Aerys’s. Schemes we don’t know the details of were being hatched, and Aerys was suspicious of Rhaegar even before the knight of the laughing tree shows up. Tensions were high at Harrenhall and it had nothing to do with Lyanna and Rhaegar, and everything to do with Aerys & Rhaegar.

Aerys doesn’t know who the knight is, I don’t think he makes the connection that his son could be honoring Lyanna because she was the mystery knight. I believe Aerys thought Rhaegar crowning Lyanna was proof that House Stark had thrown its lot in with his son over him.