Is this an API test kit ? If so, the problem may be that the test does not distinguish between ammonium, which is chemically bound, and free ammonia, which is the toxic one. This is because of how the test works. It raised the pH of the sample very high, and then reads it. This gives a 'total' ammonia reading, which can include ammonium.
The only test I know of that does make a distinction is the Seachem one.. it gives you separate readings for ammonium and ammonia.
Once you add the Prime, chloramines are neutralized, as is any chlorine and any free ammonia that may remain in the water will be turned to ammonium.
If you get consistent readings of very low ammonia, .25 or less, when you think there should not be any, chances are very good it's the 'false positive' caused by ammonium.
Edit. Btw.. chloramines gas off in the same way as chlorine does, but it takes them much longer to do it, which is why water companies add ammonia to make them. They work longer in the system.
Free chlorine is usually gassed out of water in 24 hours.. chloramines can take a week to gas out completely, passively. That means leaving the bucket of water out to age, as we used to when I was a kid keeping fish. No chloramines then to worry about. The bio filter uses ammonia from any source, but if you are treating properly with Prime, there are no chloramines left in your water when you add it to the tank.