We need more context.
"Just a squirrel" implies that a) a squirrel is unimportant, and b) that we thought it might be something more important.
"Why is our dog barking so loud? Are the neighbors' kids in our backyard again?"
"No, it's just a squirrel. You know she barks like crazy at squirrels."
"What's that noise on our roof? Is it Santa Claus and his reindeer?"
"No, it's just a squirrel."
"We have squirrels in our attic."
"Oh, you'd better call the pest control people right away."
"It's just squirrels."
"What do you mean, 'just' squirrels? Don't you realize, they're almost as bad as rats?"