Players forfeited matches and played with little preparation after taking 36 hours to get to the event.
Callum Evans, Daniel O'Connell and Chloe Thomas were all hoping to pick up qualification points for Team Wales.
"I wouldn't say it's a blow but an opportunity missed," said Jenkins.
The players were caught up in the British Airways power failure that led to the airline cancelling thousands of flights over the bank holiday weekend.
They were due to fly from Heathrow to Dusseldorf, but had to travel to Birmingham to catch a flight which was also delayed.
All three were eliminated in the qualifying stages, although fellow Wales team member Charlotte Carey is based in Sweden and was not caught up in the travel chaos.
The Wales number one topped her qualifying group with 4-0 wins over Esmerlyn Castro of the Dominican Republic and Talia Azar of Lebanon.
Jenkins, who also missed the travel problems because he flew from Manchester, said there would still be chances for the other players to impress Commonwealth Games selectors.
"It's a tough event for us, the World Championships, we're not favourites to win any medals or anything," he said.
"But they are trying to get qualification matches in order to qualify for the Commonwealth Games in Australia in 2018, so that's the main purpose of these events to get some qualification and wins.
"We've got the European Championships in September and then the World Student Games in Taiwan this August.
"So Chloe's got the opportunity to get more wins but obviously it's an opportunity lost and something she'll have to put down to experience."
Coach Ryan Jenkins hopes Wales table tennis players can still impress Commonwealth Games qualifying selectors after travel problems affected their World Championship participation.