I think you're alright. Coils get warm, in fact hot to the touch in many cases, especially on games that play more low and down, such as CFTBL and IJ. I went through a similar thing with my IJ flippers a long time ago, and I cold not figure it out. It just seemed like to the touch, they were hotter than other coils of the same WPC era. In the end, I just attributed this to the game design, and that all in all, there are more flips on some machines than others.
Take LOTR for example. I know it's a different system, but it has some much more flipper action than most sterns, and because of this is suffers more than any other machine with this same issue, coils working fine but heating up. In that case, the heat is enough to unglue the stickers for the coils. People have done all kinds of crazy mods from heatsinks to computer fans to deal with that machine. Different design altogether, but its to show that flippers can have this happen, and it's acceptable all in all.
Try taking another WPC89 flip II game you have and starting each cold, and say for the left flipper only, flip each 100 times, measure the heat with whatever you are using, then 200 times. I'm guessing this will come out to be close.
CFTBL sees a lot of quick and low play. It's hard to realize how many more times you might be flipping, but take a worst case scenario of you constantly flipping one flipper coil fast for a while, it's going to get quite hot on any machine.