I have seen plenty of threads about the Castle Thorn invisible circle during Lady Thorn's boss fight, though I have never experienced the bug myself, I do not recall it ever getting fixed. This is a pretty important mechanic to not have invisible because the only way to not die then is to follow the group and hope you're within the circle. This is not fair.

Kyne's Aegis has a mysterious problem in Hardmode on the final floor of the last boss (Falgravn). When I main tank this fight, I do not see the puddles form on the ground from his heavy attacks. This is a consistent problem, however if I die at some point during the fight and get resurrected, I will begin to see approximately 1/3 of the puddles. As a DPS, I always see the puddles. I am not sure if it is a positioning difference, a character difference, or what but I am not the only person it seems who cannot see the puddles while main tanking the fight.

Dreadsail Reef "Twins" (the first boss) hardmode has multiple invisible mechanics, one of which is on par with Castle Thorn's circle in terms of importance. All three of these mechanic invisibility issues I have seen and have heard of from many people, and they happen consistently. Firstly, the orbs summoned by the boss when he goes to teleport can be invisible, with the only thing visible being a wispy effect that is difficult to see. Some orbs will be visible, some will not be.
Secondly, the wave spawned by a weapon dying can also be invisible, which could prove disastrous if a tank needs to roll dodge (or else they will die, they can't block it) and cannot see the wave. I would say this is the most important one, but none of these should be going invisible.
Thirdly, the brand projectile marker can also be invisible. That is to say, people who get brand and must stack with someone of the opposite color could see a marker showing what direction an AoE will shoot out of them, which they should aim away from the group. That is normal. Sometimes, however, this marker is not visible at all and all that can be done is hope that the AoE doesn't shoot off into group and kill people.