Goddard appeared ginger during the Bombers’ warm-up and played just over a quarter before being handed the red vest.
“He (Goddard) was tight in the warm-up," Thompson said.
“He came off during the warm-up to stretch his groin [and] it didn't release. He tried to play and we tried to release it. In the end we weren't getting anywhere so we just subbed him."
"He's a good chance to play next week, which sounds ridiculous I know, but sometimes that happens."
In a further boon to the Bombers, Thompson said ruckman Patrick Ryder could also return from the ankle injury he suffered against Hawthorn in round two.
"Hopefully," Thompson said of Ryder.
"I think the two young ones have had enough of doing the ruck against giants. We should get him back."
It would provide welcome relief for the Bombers who were also forced to withdraw Paul Chapman (ankle), Dustin Fletcher (soreness) and David Myers (illness) before the Freo clash.
However, Thompson said all three would all return in round five.
Thompson also defended the Bombers’ decision to fly to Perth with 23 players, which left them with no one to replace Goddard after Myers was a late out.
"I suppose we have done it (flown 24 players), but it's only when someone's in doubt," Thompson said.
"We didn't know David was going to pull out ... it was literally only five minutes before we got on the bus that I found out he wasn't playing, so that's rare.”
The heat also did Essendon no favours, with the temperature climbing to 33 degrees in Perth after a week of unseasonably warm weather in April.
"I'd love to say the heat was the reason why we lost, but it's not," Thompson said.
"It was a factor but how much of a factor I'm not sure. It was a bit of shock walking off the plane and feeling the heat.
"But we still didn't play our best footy."