It sounds to me like you broke the USB port by charging internally. It's really not designed for that it should be a single battery removable mod unless I am very much mistaken. It's the reason it's recommended that external battery mods be removed and recharged externally. It's no longer going to be able to do things like download updates and whatnot, but you can still use the mod.... In the way it was designed for use, by removing the internal battery and charging it on a dedicated charger. Most folks do that by buying (at least one) spare battery as well, so that they are able to just swap out the battery as needed.
If your mods specs indicate that it CAN be charged via USB and it's still within warranty, you'd have decent case for a warranty, IF the mods specs indicate it "can" be charged via USB. If it specifically says not to (and you have) then perhaps what is needed is to continue using the mod, using an external charger, which you should be doing anyway.
Also, it's good to know some basic battery information as well as safe, authentic merchants that sell batteries and sometimes chargers.
Here are some good places for that information:
Mooch's blog | E-Cigarette Forum
Baditude's Blogs | E-Cigarette Forum
Those should help you understand batteries, and battery safety more. And, if still under warranty and the manufacturer's specs state the mod can be charged via USB, you'd have a decent case for a warranty if it is bothering you to not have the USB port, but really it should be saved for emergencies and for updates, that's mainly what it's designed for.
Best of luck,
Anna