In the settings for Safari, under advanced when I look at website data, I noticed that one particular site shows 3.1 kbs of usage. I have not accessed that site for several months and now it shows 3.3 kbs of usage. Is this even possible?

Possibly. Some cookies can be accessed and use by sites other than the one that created them. It's a common way for sites to track users, mostly for ad targeting.

Check your Safari settings and see what you have set for Accept Cookies. From Visited is usually the best compromise between function and privacy. Never will prevent it all together, but all the sites you are used to remembering you will require a login every time. Always, the least secure, might be necessary for some scenario, but I can't think of one.