The centre-back was taken off during the second half of the Shrimpers' 2-1 reverse at the Crown Oil Arena.
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And Blues boss Kevin Maher admitted Gubbins' setback was a blow for Blues.
"It was a loss because I thought he's been excellent again," said Maher.
"It's too early to know how serious it is but he felt his groin as he passed the ball out wide I think.
"We got him off as quickly as we could and we'll have to see how it settles down in the next 24 to 48 hours.
"We'll have to see how everyone is on Thursday and we'll take it from there."
Gubbins - who was replaced at the heart of the back three by Ben Goodliffe - is rated doubtful for Saturday's trip to Chatham Town in the FA Trophy.
The injury also leaves Blues short of defensive options with out of favour George Wind the only back up to the three starting.