Aguero was substituted at half-time of City's 2-1 loss to Barcelona in the UEFA Champions League on Wednesday, completing a 4-1 aggregate loss in the last 16.
The Argentine star only returned from a month-long absence with the injury earlier in March and could face another spell on the sidelines.
Tests will determine the severity of the injury, but Cousillas said the substitution of Aguero, 25, was a precaution.
"It's too early to know how long will be out. We don't think it's anything serious," Cousillas said.
"He felt some muscle pain but it was more a precaution than anything else. We'll do some tests to assess the injury."
Aguero has scored 15 Premier League goals for City this season and could play a key role as City look to chase down leaders Chelsea.
But he was unable to help his team at Camp Nou as Lionel Messi and Dani Alves struck either side of Vincent Kompany's 89th-minute goal.
Cousillas praised his players for their performance and lamented missed opportunities.
"Sometimes you score and sometimes you don't. We tried, we had our chances and sometimes you can't convert them," he said.
"We have to keep working but we're happy with our squad and happy with our performance.
"Players are human beings, not machines, and you have to go through some low times when you play so many games."
