You most likely back-fed the electrical system by turning the key on with the charger going. A couple key things to avoid this issue next time:
When you park the car and put a charge on the battery turn the battery switch off. Turn the charger off, kick the switch on, always de-activate the alarm before putting the key in the ignition. Let the car sit and warm up without the a/c, lights or any other accessory on. Let it warm up for 20mins, this gives the ecu a chance to re-learn it's parameters.
It's possibly the alarm siren has been damaged and will need to be replaced. Go through your fuse panel and check every fuse, there will be atleast one that popped and it should be for the turn signals.
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