A website with .es domain but the homepage is in English and the Spanish version is in the /es directory. Would there be any problem in the Google ranking in Spain and other countries?
I would think that would be okay, but really the only way to know for sure is to try it. Since .es is Spain which is part of a region where people travel between countries easily and speak several languages as a result, I would think that a .es site in English could perform well in England. I would say that there is a reasonably high probability of success there. How it will perform in Spain with an English home page is an another interesting question.
Here are three answers all somewhat the same that describe how Google load-balances their data-centers and decide what sites are shown where. While these answers are similar, there may be value in each.