What is the difference between the common usage of the term 'theory' vs the use of the term in the sciences?

This is a good question.

In science, theory is a complete or nearly complete explanation for a phenomenon. A theory is a self-contained framework under which phenomena occur. It is the culmination of many experiments that strongly suggest the existence of this explanation.

For instance, Einstein's Special Relativity is a clear explanation of how matter behaves when it is accelerated. Experiments end up showing that the theory is very likely to be true everywhere in the universe. Theories backed by experiments are highly respected in science and is what you want as a scientist, basically the highest level of scientific statement.

In common usage, it is pretty much the opposite. Connotations are that theories are unproven speculation. This is seen when people say "It's only a theory," meaning that isn't necessarily true.

In science, an explanation or model is a theory if it has significant support from the scientific community as factual or accurate.