Sounds like you could have scrubbed the brake pads down to their metal backing plate, if so there has been metal to metal contact which may well have resulted in the scarring and probable overheating of the discs. There are wear indicators on the pads that are designed to squeal once the brake pads get below a certain thickness, if you have driven for a extended period once these have started to squeal then damage will most likely result.
If that is the case you could have also possibly damaged the brake caliper as well due to the overheating, or caused it to seize. This could also need either a new or reconditioned caliper, in addition to a pair of new discs and full set of pads, it's always advisable to replace pads and discs in full sets i.e. new front nearside & offside.