In terms of the scrapers/counterfeits/factory overruns, those can be hard to distinguish the legitimate from non-legitimate. You'll often be able to tell a scrapper/counterfeit because the colors are weird/off, elements are missing or incorrect, or the back stamp (the copy right) is wrong/missing/damaged. Others say you can tell because they feel "rough" or the edges are sharp/pronounced. Sadly, there is no sure fire way to tell a scrapper/counterfeit. My guess is that it's easier to identify the counterfeits and the scrappers that should have been "scrapped". The factory over-runs probably look exactly like the ones shipped to Disney, so those are nearly impossible to distinguish once they're in circulation.
Regarding eBay, it is a popular source for pins, but it can be a tough place to buy legitimate (i.e., non-scrapper/counterfeits/fake) pins. The general rule of thumb is that you buy a "lot" of pins (e.g., 25-pins) and the price per pin is less than a couple of dollars each, you're likely buying scrappers. Also, if you buy pins that come in little baggies (instead of pin cards like the ones you see at the stores in WDW/DLR), those are more likely to be scrappers as well. My recommendation is to look for sellers that are selling pins still on their backing and/or unopened booster sets (also still on their cardboard backing wrapped in plastic). In truth, unless you only buy from Disney directly, it is hard to say whether you'll get scrappers/counterfeits/fakes or not.
. Sometimes if its a seller that doesn't list pins often or its a very small lot its fine. You often get what you pay for. I usually only buy in singles or very small sets. 
