I would recommend scrapping the battery and buying a new one. Its just not worth the risk when batteries are so affordable.
For a short period of time I was rotating 4 batteries in a telescoping mod. After a couple of weeks, the tops of the batteries were concave. Doesn't take much effort when the threads are a fine pitch on the mod body. Pix would help explain whether the problem is with the batteries or the design of the charger. Could also get a screw with a larger head for the mod that will prevent the condition.
A simple tweak of the contacts in the charger may fix it. I despise those chargers that have the contacts on spring loaded tracks so they fit various length batteries since they are apt to fuck up - contacts with rail or geometric distortion. I have size-dedicated or fixed charging bays, so I never had an issue with those mildly concave battery terminals.
It could get real expensive to replace batteries every time they develop signs of use that do not effect the battery's safety.
Pictures would help determine this.
Some do have vents under the + contact, but it would take some heavy abuse to distort it that much.