Because a DNA sequence and the equivalent polypeptide sequence does not contain the same information.

In the transition from DNA -> polypeptide, information is lost.

A codon will always map to the same single amino acid, but an amino acid does not map back just to one single codon. Hence, there is some ambiguity.

As phylogenetic trees, are constructed in part on the basis of the similarity between biological sequences, and polynucleotide and polypeptide sequences contains differing information - it is entirely possible to construct phylogenetic trees from the DNA and corresponding polypeptide sequence and get differing results.

@Thomas was on the right track with his comment, but as I mentioned in my comment on that post, in your case he has it backwards. Nucleotide models (which are different from a codon model) are less complex in terms of modelling evolutionary changes compared to a protein model. You're dealing with a 4x4 transition matrix instead of a 20x20 matrix. And similarly estimates for 4 nucleotide frequencies versus 20 amino acid frequencies. If your sequences are highly similar to one another, sometimes a nucleotide alignment and tree is more appropriate as synonymous changes will still be informative. However, as the diversity of your sequences increases protein alignments will become more informative because they have much more information content. You could also go to a full codon model, although I don't know if any are implemented in the software you may be using. Codon alignments can also get a little tricky to do if you aren't familiar with the methods.

To build any tree you need multiple sequence alignment.

In my opinion this post describes many detailes you need.

Multiple Alignment: Protein Or Nucleotide Sequence?

See also this discussion below - it might be helpful.

https://www.researchgate.net/post/Which_is_more_informative_a_phylogenetic_tree_based_on_alignment_of_protein_amino_acid_sequences_or_one_based_on_the_corresponding_DNA_sequences11