I would be more inclined to believe something else is causing the issue, such as something that is now running in the background etc... The charging method is basically the same with the wireless plate, except it might be a little slower, and a little warmer - but I doubt that it is hot enough to cause battery degradation. Things do get pretty warm when they charge, but if it is physically *hot* to the touch, and I mean uncomfortably hot, then you might have an issue with the phone/battery.
The only other thing I can think of that might cause a battery issue with wireless charging is if the charger itself was not sending the correct power to the battery, which is entirely possible with any charger if it is not functioning properly.
The only thing I can say with all certainty, is that my phone has been working very well and is still getting through the entire day, and a good portion of the next still - even after starting to use the wireless charger.