I'm confused

I received my September ACT scores and they are not as high as my June ACT scores. Can I send colleges just my June ACT scores? Or will they be able to see my September scores too? Would colleges know that I took the ACT test twice or would they know that I only took it once, since I would only show them one test score?

Depends upon if the colleges want your whole testing history or not. Colleges will only know that you took the test twice if you took advantage of the free test reports or if your scores are posted on your HS transcript. Most schools will accept the highest score regardless of how many times you have taken the test. Check each schools website for the particulars.