The easiest time to identify spoofers is at night when there are way less people out there, as a lot of uncertainties are eliminated. However, that would require them to be inexperienced enough to slot in the gyms and expose themselves. A random spoofer here or there actually isn't that big of a problem anymore (one person can't really do much in gyms), but organized ones with multiple accounts are. Some even try to stop people from boosting up gyms by disrupting them and then take it down.

I have faced multiple incidents where a group of us went out on a raid, took down gyms and put something easy to train against into the gym to train it up. Suddenly, a low level account out of nowhere just puts a low cp Chansey/Shuckle in to stop us from training it up efficiently, and took the whole gym down. Yes, they have accounts of other factions to disrupt with people trying to build gyms up. Even though we had 7-8 people in our group, we simply cannot deal with it. Reporting those low level accounts is futile too (not that reporting does anything at all) because they can create one in minutes.

And if the spoofers are only taking your gyms down while you are building it without slotting themselves, it is extremely hard to identify them. The only clue that you can get is people who had been in the gym before. But even so there is still quite a list of people. You can only have a vague idea of who the spoofers are by doing gyms a long time.

Oh and about bots, there are bots out there that boost up gyms and fill it up instantly. A gym can go from 0 to level 10 filled with Blisseys within a few minutes. It is impossible to fight against them because they are actually robots that won't get tired and won't stop. They usually control an area and no one can ever do anything to them.