So there's a few possible sources.
Hand heat -- which is totally normal, and will happen if you're holding the device for a decent bit of time.
Heat transfer from the atomizer -- which is also relatively normal, and is just the metal of the atomizer transferring heat through its contact with the mod.
Heat from the batteries -- which is not normal, and is bad. Substantially bad.
Next time the mod gets hot, pop the batteries out or just feel them. Are the batteries themselves hot? Feel the atomizer, is the atomizer hot? Have you been holding the mod for a long time (5+ minutes)?
You should be able to narrow down the exact cause of the heat and then you'll be able to address it (or not address it) appropriately.
ETA: There could also be heat from the internals of the device, but if the device is operating properly that's really not likely to be the case. PCB's and stuff are more likely to simply stop functioning than overheat, and if they do overheat they're going to go up in a blaze of glory rather than slowly heat up over a long period of time.