The reason why isn’t clear, but the new Daleks have mutated in some way
In the episode, when the Doctor is reunited with the fam and does a scan for Dalek DNA on Earth, she says this:
Dalek DNA trace, Japan. Osaka. Well, sort of. Not an exact match. Ah, it's corrupted. I can't quite make sense of it.
Then, when the Dalek Death Squad arrives, they declare:
Scan determines rogue creatures below! Mutated Dalek DNA detected!
And then when they meet the cloned Daleks in the human-built travel machines:
DEATH SQUAD DALEK: Identify!
DALEK DRONE: Dalek!
DSD: Incorrect. Scan detects anomalies. Dalek DNA merged with human traces.
DD: We have mutated to survive.
DSD: You are impure! The Dalek race must have purity! Exterminate!
DSDs: Exterminate the impurities! Exterminate the impurities! Exterminate the impurities!
THE DOCTOR: That's the thing about Daleks. For a race born out of mutation, they're pretty obsessed with purity.
And finally, the last remaining cloned Dalek makes a case to the Death Squad:
I can be purified. My genetics can be modified.
So it’s not stated why, but it is clear that the Daleks grown and cloned from the traces of DNA found in the Reconnaissance Dalek’s shell have mutated and no longer possess “pure” Dalek genetics. The script doesn’t say this is because of the humans they were fed on, but it’s implied by the “human traces” of DNA mentioned by the Death Squad. It’s not unreasonable to think the Dalek DNA remnants were fragmented or incomplete, requiring parts be filled in by something else - and human DNA was the closest fit. It may also have been altered due to the use of primitive (by Dalek standards) human cloning technology, or it could even be something to do with the long imprisonment of the Reconnaissance Dalek.