In this scan you provided, at the bottom left, Suigetsu said "That's weird I'm sure it was around here". And this sentence is very worthy of attention, because it clearly implies Suigetsu did the test with the wrong DNA sample .
Sorry about "clearly implies", let's replace it by "hinted about". First, Suigetsu expected Karin's DNA sample to be there, but he was surprised by not seeing it where expected, which HINTS something unusual happened. Which leads to the belief that it wasn't Karin's DNA, but he picked the wrong sample for the test.
unless she was keeping something of Sasuke's in that desk, it could only be hers'. And it wasn't like he said "this probably belongs to her". He seemed positively sure, and i think it would only make sense for Karin's genetic material to be the thing he compared Salad's against, seeing as though he already knew who the father was. So testing Salad's genes against Sasuke's was pointless; unless Suigetsu was smart enough to know how how to work a paternity machine but somehow be stupid to confuse one person's DNA for another.
He didn't compare her DNA to Sasuke's knowingly. What he picked must have been Sasuke's DNA sample and Suigetsu compared it to Sarada's, thinking it was Karin's DNA sample.
