I assume you mean and then format the HDD?
Is it 'bad' to clone a drive? No. That being said, you clone it identically, so you take the good/bad/indifferent. Registry errors etc all clone too - so a clean install is preferred.
Formatting a drive, in & of itself is not a bad thing either. Excessive formatting though (daily/weekly/monthly etc), can impact the lifespan of an SSD - HDD's, not so much.