European champion Hughes clocked 20.12 seconds in the 200 metres final at the Alexander Stadium on Saturday night but finished behind reigning champion Jereem Richards.
The Trinidad and Tobago star ran a Games record of 19.80 secs.
It comes after Hughes was disqualified after winning the 200m at the Gold Coast in 2018.
He was ruled to have impeded Richards before they crossed the line and had an appeal thrown out, having already done a victory lap, with Richards handed the title.
Meanwhile, Hodgkinson targeted a golden finale to her season after being beaten.
She could only take silver in the 800m as Kenya’s Mary Moraa upset the favourite to claim victory.
The Kenyan finished third behind Hodgkinson when the Briton also took silver at the World Championships last month.
Scotland’s Laura Muir clinched bronze as Moraa’s run – which saw her lead the first lap before falling to last with 300m to go and then storm back – stunned the Alexander Stadium.
Hodgkinson ran one minute 57.40 seconds but could not hold off Moraa – who retook the lead on the home straight – and is now eyeing a big finish at this month’s European Championships in Munich.
“I’m definitely determined to win a gold, three more warm-ups and cool-downs to do and the season is almost finished,” she said.
“I really wanted the gold, worlds was definitely the hardest and I thought I was going to win today but I guess it wasn’t meant to be.
“Mary went off quite hard and there was a bit of argy-bargy in the corner so I needed to keep my position. I don’t really know what Mary was doing, to be honest. I was focusing on myself.
“It happens I guess. I think we had quite similar strengths in the last 200m and my plan was to be ahead of her and hopefully she wouldn’t catch me. She did but it is what it is. I’m pretty gutted.”
Moraa, who won in one minute 57.07 seconds, admitted she went off too quickly and almost gave up on a medal.
“My plan was to go through quite fast in 57 or 58 seconds but after 300m I realised I was going too fast as I was running at 56-second pace,” she said.
“I lost hope because everyone went past me. I was last. But when I got to 200m I started to close the gap and with 120m to go I was counting 1-2-3-4 and I started to think I could win a medal. I kept pushing.”
Muir took her first Commonwealth Games medal and is also in the 1500m final on Sunday. She said: “My coach told me to go out hard, and I thought I did – but I was still miles off it. These girls are fast. I was in fourth with 100 to go and I thought, ‘no way, no way’. But my coach said run all the way to the line.
“I was so determined, doing the double, that I was not going to waste running the 800 and not getting a medal.”
Earlier, world champion Wightman admits he did “as good as I could have” as his hopes of a stunning summer hat-trick ended after coming third in the 1500m.
The 28-year-old Scot took bronze behind Australia’s Oliver Hoare and Kenya’s Timothy Cheruiyot after being passed on the home straight.
He was hoping to continue his unique treble quest – after July’s World Championships victory – but must now refocus for the 800m at the European Championships.
“That was as good as I could have done,” said Wightman, who ran 3:30.53.
“I didn’t want to be a pedestrian and be running for minor medals. I wanted to make a statement but I didn’t feel anywhere near as good as I did a couple of weeks ago.”
Wightman stunned Olympic champion Jakob Ingebrigtsen to win in Eugene last month as dad and coach Geoff commentated on the race at Hayward Field.
Wightman senior was again the announcer at the Alexander Stadium and watched as his son made a move with around 300m to go – but he was overhauled.
Soon after, England’s Nick Miller won gold in the hammer with a throw of 78.43m to defend his 2018 title.
England’s men’s 4x100m relay squad of Jona Efoloko, Harry Aikines-Aryeetey, Nethaneel Mitchell-Blake and Ojie Edoburun won their heat in 38.48secs to reach Sunday’s final.
Asha Philip, Imani-Lara Lansiquot, Bianca Williams and Ashleigh Nelson progressed to the women’s final by finishing second in their heat in 42.72secs.