Last week there was a significant amount of controversy over whether the new iPad generated too much heat. Reports about just how hot the new iPad gets have varied pretty widely, with the most recent data suggesting that the amount of heat it puts out is comparable to its Android-based rivals.

In the midst of the ridiculously-named “heatgate” controversy, news of another problem with the iPad began circulating. It turns out that the iPad’s battery keeps charging for as much as two hours after the battery indicator reads 100%. This is potentially a bigger problem than the heat issue. Features like the retina display and 4G require a lot of power to operate (more than double the power, in fact), and Apple has had to make a major upgrade to the iPad’s battery to keep 10 hours of battery life that the iPad 2 boasted. If the battery isn’t charging fully when it says it is, people are going to be getting less from their iPad’s battery than Apple said they would.

Apple, however, has an answer for those who are concerned about the battery issue. They acknowledge that the battery isn’t quite full when the indicator reads 100%. Rather, it’s full enough to give you the promised 10 hours of use. That, at least, is what Apple told CNBC reporters in the video below:

So there you go: when your iPad says it’s “100%” charged, it’s actually just charged enough to give you the performance Apple promised. All well and good, right? Problem solved, right? Not exactly. Note that last bit about how overcharging the battery can damage it. Think about that for a second: if what Apple says is true, then they basically expect you to watch your iPad charge until it reads 100%, and then immediately take it off, lest it damage the battery. For a device that charges quickly, that may not be a problem, but the iPad doesn’t charge quickly. It takes somewhere in the neighborhood of 2-3 hours to reach 100%. Because it takes so long, a lot of people plug in their iPad overnight to charge. Those people, according to Apple, are harming their battery by leaving it plugged in after the battery indicator hits 100%.

Now, it’s worth emphasizing here that the iPad only continues to draw power for another two hours after the indicator hits 100%. After that it stops drawing more than a minimal amount of power, even when plugged in. The iPad stops itself from charging at that point. What that means is that rather than stop charging when it reaches 100%, the iPad allows itself to continue charging to such a level that it damages its own battery.

That’s a big problem, according to Dr. Raymond Soneira, president of DisplayMate and the one who discovered that the iPad keeps drawing power after it says it’s fully charged. What’s more, it’s Apple’s problem, not the consumer’s. After CNBC’s report, which aired Friday afternoon, Soneira updated his study with a reply to Apple’s statement. He calls Apple’s response “poorly thought out damage control,” and said that it was Apple’s responsibility to deal with the issue by rolling out a software fix as soon as possible. Check out his update below:

While my interpretation is that this is just simply an issue of correcting the on-screen battery indicator so that it matches and agrees with what the battery charging hardware and software actually do, Apple has put forth a rather shocking reverse perspective that the on-screen battery indicator is instead the correct one. As reported by Jon Fortt of CNBC: “Apple is saying… if you charge it more than [when the battery indicator reads 100%], you could actually harm the longevity of the battery.”

Damaging the longevity of the battery is then exactly what the new iPad’s internal battery charging hardware and software are doing since it is their responsibility to properly control and manage the battery recharging process. It’s pretty obvious that if the new iPad knows that it is fully charged then it should automatically stop the charging! So according to Apple the new iPad is configured to damage the longevity of its own battery if it isn’t manually disconnected from the AC charger when the 100% indicator appears. Anyone that recharges their iPad unattended, especially overnight, will be doing this.

While Apple’s remark might apply to recharging dumb battery operated toys, the new iPad is a very sophisticated and expensive computer device that is fully capable of properly controlling and managing its own (rudimentary) battery charging process. Perhaps Apple should instead graciously accept my interpretation and rescind their own remarks, which sound like very poorly thought out damage control. Otherwise they need to immediately fix the iPad battery charging algorithm or they may be held responsible for replacing all iPad batteries. Which one will it be?

Few will deny that Apple makes some pretty amazing products. What Apple does not, apparently, do well is deal with problems that those products have after they release. In 2010 it was the badly mishandled “antennagate” issue with the iPhone 4, which ultimately led to a class action lawsuit. Apple settled the suit, agreeing to give everyone who purchased an iPhone 4 either $15 or a bumper case for their iPhone. This has all the earmarks of a similar scandal. In effect, Apple shipped the new iPad with a software glitch that (they now say) has the potential to damage the iPad’s battery, and their response has effectively been to tell users not to let their iPads charge after the battery indicator reaches 100%.

Whatever happens in the next few days or weeks, you can bet that the statement to CNBC will not the the last we hear from Apple on this issue. Whether they actually make another statement about it or not, you can probably expect iOS 5.1.1 to show up in the not-so-distant future with a fix.

What do you think of Apple’s statement about the battery problem? What should Apple do to fix it? Let us know in the comments.