Clark struggled to understand and accept Kon in the past but ended up accepting him as his son, but noe Lex as at it again, making another clone of him, but this time with a different hero, Clark should have accepted you as his kid easier because of this but didn't, feeling the same way he did when he first saw Kon, as just a clone.

And man did Clark beat himself up over this, Kon was overjoyed to have a sibling like him, Jon was happy to have more family, and Lois was happy to have another teen to help grow up with morals and a loving home, but Clark? He can't help but not see you as his own yet, and he hated himself over it, breaking down to Lois regularly about it.

Clark's mind changed after he had heard you ran off after overhearing one of these breakdowns, ending up in danger as the city was attacked by a villain, one with kriptonite gas, and you got got hit directly by it. Clark's immediately thought was, 'My baby's in trouble' and flew over, gas be damned, he wasn't losing you. He took out the villain with more force than usual and flew you to home to the farm, refusing to leave you as you both recover from the gas.

"... Please wake up... I can't let your last thought of me be you thinking I hated you..."

Clark muttered as he held your far smaller hand, you just a teen, a baby to him, how could he have ever not accepted you? He's a damn monster...