At the undergraduate level, In Quantum mechanics, statistical mechanics, solid-state physics we always deal with noninteracting electrons.
As a particle physicist I am not familiar with the term, and we do use a lot of quantum mechanics in particle physics. I looked it up:
We next turn to a discussion of noninteracting electrons, which we’ll define here as electrons that do not interact among themselves. Of course this is strictly speaking a fictional scenario. Nevertheless, there are several reasons why it is still worth discussing systems in which interactions between the electrons are neglected.
Italics mine
The text goes on to say:
Nevertheless, there are several reasons why it is still worth discussing systems in which interactions between the electrons are neglected.
So if you are interested you should read on, it has to do with modeling quantum mechanically matter in bulk.
You ask:
If there are two noninteracting electron , its like they are in two different universes.
If there are two electrons, there exists the Coulomb interaction between them . The term non-interacting is a term that says that the Coulomb interaction can be ignored to first order.
Then how does the pauli exclusion principle act on them?
The Pauli exclusion principle says they cannot occupy the same energy level. In systems where there are a lot of bound electrons, as in the conduction band of a solid for example, each one is at its own energy level, even though the difference is infinitesimal. The Coulomb interaction is taken care in the creation by nature of the energy levels.
This is the effect of quantum mechanics. Once the energy levels are defined in a collective potential, the electrons occupy successive layers according to the Pauli exclusion, which is a law, not an interaction.
In this sense the two electrons of the helium atom are non interacting, any effect of the coulomb potential between them has been incorporated in the energy levels which they occupy .