Wireless chargers are inherently less efficient than wired ones, so some heat generation is pretty much unavoidable - it's just physics. The electromagnetic field that transfers power through the air and your phone's case has energy losses, and that wasted energy turns into heat on both the pad and your phone. A little warmth is totally normal and nothing to lose sleep over.
That said, there's a practical difference between "warm" and "hot enough to be uncomfortable touching." If your charger is getting uncomfortably hot, try moving it to a spot with better air circulation - don't tuck it into a drawer or under your pillow. Also, if your phone case is thick or made from dense material, it might be insulating the whole system and trapping heat. A thinner case or no case at all can actually help dissipate things better. Overnight charging tends to amplify the heat issue since the charger's working for hours, so if you're worried about long-term effects, consider disconnecting once your phone hits 100% rather than leaving it sitting there all night.
The battery itself usually doesn't suffer much from the charger being warm - phones have built-in thermal management that throttles charging if things get too toasty. Your charger pad is more at risk from sustained high heat than your phone is, but even then, they're designed to handle this. Just make sure it's in a breathable spot and you should be fine.