The words universe and atom originally had very specific abstract meanings. Universe referred to “everything that exists” while atom referred to the “smallest indivisible constituent of matter” (from the Greek philosophy of Atomism). Over time these abstractions became concrete in their meanings.
As the science of physics progressed people came to have assumptions as to how big the universe or the atom would prove to be. When they thought this limit was reached, they began using the abstraction to express the concrete. Of course, science proved those limits to be wrong; today, an atom refers to a concrete piece of matter that is hardly the smallest, and universe has come to refer to an object which is “expanding” and therefore can hardly include all of existence. The word universe has even spawned terms such as “multiverse” or “parallel universe” which are clearly in contradiction with the original abstraction.
The best way to keep these equivocations clear is to ask yourself this question whenever they appear in an argument: does this person intend to express an abstraction or a concrete “real-world” object? You may find that the person making the argument isn’t clear on it himself.