Scott-Morriss was substituted as a part of a triple change in the 66th minute.
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And Blues boss Kevin Maher has confirmed it was an enforced alteration.
"He had a tight hip," said Maher.
"He was feeling it.
"At half-time it was stiffening up but he wanted to get back out there for the second half.
"He was feeling it tightening up and we couldn't afford to take any risks.
"We'll have to see how it settles down."
The Shrimpers head to Altrincham this weekend where Scott-Morriss will be walking a disciplinary tightrope if he plays.
The 28-year-old is on nine yellow cards with Saturday's game the cut off for 10 cautions resulting in a two match ban.