If you are using the API test kit, Prime and Amquel can affect the reading. I had a 75 gallon set up and was having the same problem..I use Prime and Amquel almost exclusively. My tap water was clear...surprise there
. The fish werne't in any distress but I couldn't get rid of that .25 reading. I did a search to both API and Prime, sent e-mails to both. API admitted that the test is sensitive to both Prime and Amquel. When I switched to Stress Coat as a test, the Ammonia reading went to 0.
It may be something to try as well as the other suggestions.