You will find one of my earlier answers useful.
Imagine I had a dataset containing observations on people who suspected that they had the flu. In the data are two variables, $T$, their body temperature, and $V$, the viral load of influenza (measured with a lab test). You run the following regression:
\begin{align}
V = \beta_1 + \beta_2T + \epsilon
\end{align}
You find a large, positive value for $\hat{\beta}_{2,OLS}$. You conclude that a good way to treat the flu is to put people in ice baths to reduce their body temperature. Right?
Not right. In fact, idiotic. Both the person's viral load test result and the person's body temperature are being affected by whether and how badly they are infected with influenza. In fact, the following regression is probably closer to right:
\begin{align}
T = \alpha_1 + \alpha_2V + \nu
\end{align}
Your body temperature is affected by how much virus you have.
As I say in the earlier answer linked above, we run regressions for two totally different purposes. First, we run them for prediction. If you wanted to predict viral load based on body temperature, the first regression above is a fine way to do it. If you wanted to predict temperature based on viral load, the second one would be a fine way to do it.
Second, we run them to understand causation. If my question is "How much would viral load fall if I reduced a patient's body temperature by 1 degree (in an ice bath)," I can run my first regression above. But the answer it gives me is only right (consistent) if the equation captures causation properly. If the causation, out in the actual world, runs from body temperature to viral load (and not the other way, and not from some third factor to both temperature and viral load).
If my question is "How much would temperaure fall if I reduced a patient's viral load by 1 unit (say via an anti-viral drug)," I can run my second regression. But the result it gives me is only right (consistent) if the equation captures causation properly. If the causation, out in the actual world, runs from viral load to body temperature (not the other way, and not from some third factor to both temperature and viral load).
In your example, I assume the business question you are interested in is something like "What will happen to a store's market share if I increase its size by 1000 square feet?" If you try to answer this question with the regression you propose, you will, I am almost certain, get an answer which is much too big.
What do I mean, too big? Suppose you got a coefficient of 10 (measuring size in thousands of square feet and market share in percents). That would appear to say that increasing store size by 1000 square feet would increase market share by 10 percentage points. If you then run an experiment, out in the real world, in which you increase half (chosen randomly) of the stores' sizes by 1000 square feet, the increase in their market shares (compared to the not-increased stores) will be less than 10 percentage points.
How do I know this? Because I am confident that there is a third factor which affects both store size and market share. That third factor is the demand for that store. Somebody decided to make store 1 7400 square feet and store 2 4400 square feet. He did that because he thought store 1 would have a higher demand than would store 2. Likely, store 1 also has a higher market share than does store 2. Again, because it has higher demand. So, size and market share will be positively correlated. But not only or even primarily because size causes market share. More because market share causes size.
Wait, you say! If I can use my regression for prediction, then I'll use it to predict market share for a 6000 square foot store and then again for a 7000 square foot store. The difference in the two predictions tells me how much market share would rise if I make the 6000 square foot store 1000 square feet bigger!
No, it does not work that way. The prediction you make using estimates from dataset is only good for circumstances like the ones in the data. If the variation in the data in store size came from Ricardo Cruz doing experiments, then the method described in the previous paragraph will work fine. On the other hand, if the variation in the data in store size come from some guy making guesses about "how big a store do we need here," then these predictions are not valid in a new, different dataset where the variation in store size comes from Ricardo Cruz doing experiments.