Yes, or it was at least with me. I used to live full-time in Canada and when I came down before I became a Canadian, I used to have to get a new I-94 every three months. A few times a CBP officer did remind me that if I wanted to live permanently in the US, my husband had to file for a spousal visa. I said to them, I am well aware of the rules and this visit is temporary, I have work and responsibilities in Canada which cannot be abandoned. I was let in without any issue at all. My visits were never more than a couple of days at a time and I had a good history of travel compliance. Indeed I ultimately came here on a CR-1 visa, I still have those responsibilities and work in Canada despite living here, so AoS was never an option for me regardless of my intent. xD
And yup, the process can take two years, it may take less, or it may take more. Some folks end up waiting a very long time indeed, but that's mostly nationalities of high-risk countries who get their petitions sent back to USCIS or stuck in Administrative Processing.
Whether you were flagged may depend if you were referred to immigration secondary or not. They may have put a note on your file that there's a risk of immigrant intent there. If it was a customs referral, I have my serious doubts that they did. Anyways, so long as you're keeping your visits short and have work/responsibilities in your country of residence I think your future visits to the US should be fairly uneventful from an immigration perspective, although it is ultimately up to the CBPO you get.