I am able to upload a custom character and apply animations and everything looks great in Mixamo, however if I export using the default FBX option and import into Maya, the model only exports with 1 bone and not the expected joint hierarchy.
then Maya is not reading your Fbx file correct... try loading it into some other 3D software or share the file and I'll test it at my end
What version of Maya? Which FBX (maya)?
Maya 2020.4 and the default fbx plugin that installs with 2020.4 which is FBX v2020.1.1