Others have already replied on several reasons as to why. I will put it this way, the electronics in a mod are made to be small and portable. If you think about it, on the tiny circuit board no larger than a standard cigarette lighter, and no wider than a pencil, it has the functions of an ohm meter, LCD display and control output, charging circuit, and voltage/wattage regulator... all those functions on a circuit board that small and require so little power..... something has to be compromised. For that reason, I only trust the electronics on an Ecig for one thing, to vary the wattage and allow me to vape... I do not trust it for any sort of charging, even if they say they can.... especially for more than one battery.
I use an external charger. The added benefit is, I can charge one set of batteries while I vape with the other. I just make sure I don't keep the batteries in the charger once they're done charging. Another thing people don't mention, is that you may not know how warm the batteries are when you plug your mod in to charge. Taking the batteries out to charge allows you to feel how warm the batteries are, and it also serves as a reminder to occasionally clean the contacts and vent holes from time to time. Baditude has listed some very well known battery chargers, and I'd have to second his recommendations. I have an older styled Nitecore I4, and it's served me well. It is basic compared to a similarly priced Efest LUC charger, so like he said, you get more bang for your buck.