I can think of no reason that a slowed flow rate would cause an increase in temperature. I would actually expect, if anything, a slight decrease in certain areas of the tank due to lack of water circulation. I don't think this is related to your filter.
A few questions. Is your heater adjustable? If so, crank it down, even if it says it's at the correct temperature.
Is your heater preset? If so, is the amount of watts appropriate to your tank size? If the heater is supposed to be good for your tank size, I would worry that it is breaking and as much as I hate to say it, you might want to look into buying a new one.
Adjustables are more expensive, but they're really nice to have around in case you need to treat a disease by raising or lowering temperature. I'd say it's worth it.