Usually it's the other way around. That's common. More income = more tax and usually less refund.
Because you only get one standard deduction and personal exemption (or 2 for Joint), no matter how many W2s you put in. Turbo Tax starts out by giving you the Standard Deduction. You entered more income when you entered the second W2 but you didn't enter more deductions. And each job only withheld taxes like it was your only job for the year. You might want to adjust your withholding. Also as you add more income you might not be getting as many credits as before like the EIC credit. And it was probably giving you the EIC credit until you went over.
See,
https://ttlc.intuit.com/questions/2273878-why-did-my-refund-drop-when-i-entered-another-w-2
