I wasn't around for the 6.0 era, but I have a list of more recent judging stuff that gets under my skin. This is not intended as shade towards any of these skaters; many of my faves get overscored, so this is not a list of skaters I hate or anything. Most of my complaints are actually about the margin of victory, not the result itself.
Bradie Tennell winning 2018 US Nationals over Mirai Nagasu. Bradie did an amazing job, but I think the US was eager to dish out high scores for her because they needed a new it-girl. Mirai brought her A-game that night and I think the judges really held back on her scores. Not to mention, Ashley Wagner's PCS were ridiculously low that night and I'm still bitter.
Satoko Miyahara winning 2018 Japanese Nationals over Kaori Sakamoto. Kaori consistently receives low GOE for her jumps even though they are some of the best in the world. Satoko is a beautiful skater but she lacks that it-factor for me, and there is simply no way she should've beaten Kaori by several points.
Tarasova/Morozov winning the 2017 European title over Savchenko/Massot by such a large margin. Savchenko/Massot struggled in the SP but I think they were underscored. In the free skate S/M went clean and T/M struggled with a lift, however S/M only won the FS by 2 points over T/M. S/M had the superior free program that year, so I definitely think they should've won Euros that year.
Carolina Kostner winning 2013 Europeans over Adelina Sotnikova. I adore Carolina, but she was heavily held up with PCS despite making major mistakes. I find it funny how everyone raked Adelina over the coals for being juniorish and unpolished, but that has become the new norm just a few years later.
Papadakis/Cizeron's 2015 world title over Chock/Bates and Weaver/Poje. P/C have grown into a gorgeous team, but I don't think Mozart was one of their strongest programs (compared to, say, To Build a Home, which felt much more emotional and mature). Chock/Bates' FD wasn't particularly compelling that year, but they are so technically sharp. Weaver/Poje had the best program of the three IMO. However, I think the scores were so close that it became a matter of personal preference.
Alexa and Chris Knierim winning 2018 Nationals over Tarah Kayne/Danny O'Shea. The Knierims are usually the superior pair and they earned their Olympic spot fair and square, but with their mistakes I can't justify them winning. Kayne/O'Shea only had one major mistake, and they had two very strong programs overall.
Volosozhar/Trankov winning the free skate at the 2014 Olympics over Stolbova/Klimov by such a large margin. V/T had been the clear no. 1 in Russia and they had huge momentum going into Sochi, which snowballed their scores all season, whereas S/K were a new pair with little major international experience. However, on that night, V/T got positive GOE for two-footed throw landings whereas S/K went clean, and the PCS gap (77 for V/T versus only 71 for S/K) was too large. V/T deserved their win overall, but the margin of victory still smells fishy to me.
Alina Zagitova beating Wakaba Higuchi at 2017 Cup of China. Alina is an amazing technical skater, but she made big mistakes in the SP while Wakaba went clean and still won. I just don't see it.
Javier Fernandez winning 2015 Cup of China over Adian Pitkeev. Javi was just all over the place, missing jumps, and Adian had two very strong performances. I understand that Javi is a great performer and puts on a fun show every time, but charming smiles do not un-pop quads. Javi deserves huge PCS for being The Greatest Showman, but his skating skills lag behind a bit, and the judges seem to overlook that because he is so entertaining.
Duhamel/Radford beating Stolbova/Klimov for the bronze medal at 2017 GPF. Okay, I love Meagan and Eric with all my heart, but mathematically it doesn't add up. In the SP, S/K skated with clean elements (she had one fluke fall but it didn't affect the choreography), while D/R made a few technical mistakes, but D/R received higher PCS (IMO, S/K have the better skating skills). I think if the SP had been scored correctly, it would've affected the medal standing. However, I love both of these teams, so I don't really have a problem with it.
Sui/Han beating Duhamel/Radford at the 2018 Olympics by 5 points. D/R really threw down the gauntlet, while S/H's performance felt a little tight (understandably so because they were trying so hard to beat Savchenko/Massot). I feel like the judges forgot D/R because it had become a showdown between S/M and S/H. S/H had the best SP of the event and S/M had the best FS, but D/R had the best overall performance. I think S/H were held up a bit on TES despite missing both side-by-side jumps and losing levels. On PCS I think it was fair - the only thing I'd change is Tarasova/Morozov getting 74 for that Candyman crisis!
Hubbell/Donohue beating Chock/Bates for the 2019 US National title. For me, C/B had much more sparkle, and they skate with controlled power, while H/D (particularly Zach) seem to tear across the ice with unchecked speed, which I don't find aesthetically pleasing.
Chock/Bates finishing third at 2018 Nationals. I think they were very underscored in the short dance and they couldn't make it up, even with the beautiful FD.
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I'm sure there are more, but those are the ones I can think of immediately.
Sotnikova over Kim wasn't right IMO, but I don't see it as the greatest injustice of the sport. It's the classic example of the Russian wonder kid with big jumps beating a more refined older skater. These days, it happens all the time. I think it was only such a big scandal because we didn't know that was going to be the new status quo.
While I prefer Kwan over Lipinski by a mile, I think Lipinski earned the 1998 gold based on her technical content. That's about it.