It's not clear to me which charger you were using when you got the warning, but one thing you should know: Apple chargers and the rest of the world of non-Apple devices are only partly compatible. I'll try to keep this short:
The USB standard was originally developed for data transfer with computers, not charging devices. As such, it is a low power standard. Computer USB ports are generally limited to 500 milliamps (mA) output. A device like a cell phone can draw up to 1,000 mA (or occasionally more). Tablets generally draw 2 amps or more. Plugging a device that draws 2 amps into a computer USB port will fry the port. So device makers needed to come up with a way to detect whether the device is plugged into a computer, and limit the current draw, or into a charger, and allow the device to draw as much as it wants.
If you look at a USB plug, you'll see it has 4 contacts. The outer 2 carry power, the inner two carry data. When plugged into a charger, the inner two are not used, since the device only needs power. So the industry came up with this approach: high output chargers short the two contacts for data together. Phones and tablets can detect this, and decide what charging mode to use. Apple, of course, came up with it's own solution. It accomplishes exactly the same thing, but because it's proprietary they were able to patent it and charge royalties to anyone who wants to make an iDevice compatible charger.
Why does this matter, you're wondering? Because when you plug your Galaxy S3 into an iDevice charger, it doesn't detect the shorted data connections, and charges only at the slow rate, which is about 300 mA. When plugged into it's own charger, or any other non-iDevice charger, it will charge at a higher rate of about 800 mA. At the low charge setting, it may not keep up with cpu and screen intensive use of the phone, so you battery continues to drain. I assume that Apple devices charge only at the slow rate when plugged into a non-compatible charger, too, but don't know for sure.