Why did the real-time PCR yield Ct values < 12?

You probably used too much template. Try less input RNA for reverse transcription especially if the higher end of the recommended range had been used previously. Or use a smaller volume of template per PCR reaction or use diluted template, but do not use less than 1 µl of template per each 25-µl miRNA PCR array reaction. Remember to use the same volume of template in each reaction.