Yes, this is very likely, and very common. In fact, if anything, I'm surprised you're able to get any refund at all!
It's impossible to give an exact answer without knowing the full details of the fares purchased, but this will almost certainly be the combination of two or three different factors :
Most airlines charge more for one-way flights than international flights. For example, picking random dates in March you could fly on Turkish Airlines from New York to Istanbul return for around $900. However booking exactly the same flight on the outbound as a one-way costs over $1000.
When you attempt to cancel your return flight, the entire ticket will be repriced due to the change from a return ticket to a one-way. As a result, the price of your outbound flight will change - even though you've already flown it! Whilst this may seem odd, it actually makes sense as otherwise you could workaround the first point by... well.. by doing exactly what you're attempting to do!
Depending on the fare rules, you will often pay the highest change fee of ANY flight on the ticket, not just the one you're trying to change. So even though it's the return flight you're trying to change, it's possible you'll pay for change fee for the outbound flight as it will likely be higher (given it's a lower level of fare).
In this case, points 1 and 2 are definitely playing a part in what you're seeing.
For point 3, most Turkish fares do actually allow you to pay only the change fee relevant to the leg you're changing. eg, from a typical TK fare rules :
WHERE THIS FARE IS COMBINED WITH ANOTHER FARE AND ONLY ONE FARE COMPONENT IS CHANGED
THE PENALTY CONDITIONS OF THE CHANGED FARE COMPONENT WILL APPLY
WHEN MORE THAN ONE FARE COMPONENT IS BEING CHANGED
THE HIGHEST PENALTY OF ALL CHANGED FARE COMPONENTS WILL APPLY
So as a general rule you'd only pay the change fee for the return flight. However, based on the 2nd point above, canceling your return flight will result in a reprice of the outbound flight, which may be seen as a "change" to that flight, so it's not clear to me which change fee you would be charged.
Keep in mind that all of this is happening because you're looking to cancel the return flight. If you were to simply move it to another day then it would be a different story as the itinerary would remain as a round-trip, and thus the outbound fare would not be repriced (Presuming you stayed within the condition of the outbound ticket, such as any minimum/maximum stay provisions)