Taxation rate is different for different amount of money you make throughout the year. If you make 55000 P.A that means you are in the tax bracket of 25%. And (25% of 55000)=13750 is already paid by you to the government. 
Calculation goes like this

First $8,025 dollars you made is taxed with 10% rate = $ 802.5(a)

Then $32550 of the money $32550-$8025 with 15% rate=$3678.75(b)

Again $55000 of the money $ 55000-$32550=22450 with 25% rate=$5612.5(c)

sum(a)+(b)+(c)=10093.75 is the actual amount you need to pay but you already paid 13750.So you will get the difference amount as your tax return.

It looks like one of those company might have kept you in different rate than 25% if that rate is less than 25% then the Tax amount you already paid to the government will be less and if its less than 10093.75 then you need to pay government back the money.
I am not into accounting I might be wrong  refer to this website