Along with fever when she has tummy problems too its better to give her Acetaminophen
syrup for fever. You may give it when temperature is more than 100 ' F.
One or two dose of motrin will not cause a problem. Do not worry.
Her tummy ache may just be due to gastritis
or she might be developing a gut infection. She might need medications like Lansoprazole
that will help for her gastritis and enzyme preparations like Neopeptine
Since you say, her oral intake is poor, my suggestion would be to have her seen by Pediatrician
and get her treated.
Wish your kid a speedy recovery.