QIK will try to clear the seats all the way through to the final destination. So when an agent clears seats out of LGA, if the flight is full out of CLT, then the agents need to unseat the through nonrevs and relist them there... it's a pain in the butt for the through city.
In any event, if you were listed as LGA-DEN, then it is entirely possible to see why the agent said he was sorry that he didn't have two seats together. When QIK clears you a seat, it is looking at the whole flight including the stopover in CLT as to what seats are available and will only clear you a seat that is available for both segments of the flight. It won't allow the agents to simply change your seat per leg. When QIK clears you, it clears you for both segments as though it were only ONE flight. There is a way to split route seat.. or in other words, put you in two different seats for each leg, but it is complicated and does not work half the time in QIK and also, it is used for revenue passengers only.