Not a purebred?

What he means is that the English Mastiff was probably reintroduced much later into Marmaduke's bloodline after the Dane became an established breed. After a breed is officially recognized and established, breeders stop introducing other breeds to the lines and just mate the new purebred dogs together. Mating outside the breed, even if it was from a dog that originally went into it, is considered a cross and the resulting pups are no longer considered purebred.

I'll give you an example. Labrador retrievers are believed to be bred from the now extinct St. John's Water Dog, which itself is believed to be made from a mixture of spaniels, setters and other retrievers. Once the Labrador Retriever became an established breed of its own, the only way to have a purebred Lab is to breed two Labradors together. If you were to today breed a Labrador with a spaniel or a setter, despite them being instrumental to establishing the Labrador breed, the resulting puppies would be considered mixed breeds. You wouldn't have Labrador Retriever puppies, you'd have Lab-spaniel or Lab-setter puppies. Any puppies that those mixed puppies have in the future would also be considered mixed, even if they had puppies with other purebred Labs.

So in Marmaduke's case, it's possible that Phil's boss believes that Marmaduke is not a purebred Great Dane, but is probably a recent Dane-Mastiff mix (possibly from a mixed parent or grandparent).

Though honestly, I'm not sure how Phil's boss considered himself an expert on identifying dog mixes just by looking at them (it's not like he's a Dane breeder or a dog show judge in his spare time). It's all very subjective, and it's obvious to me that the guy didn't have a clue what he was talking about.