Thank you for all of the awesome replies everyone.
To add a bit of context. I purchased a new second hand bike and that was when I got the bike fit, new stem, new handlebars. A month later I got new shoes. The cleat position was traced off my old shoes and replicated on my new shoes. I use Shimano yellow cleats on dura ace pedals. I also switched the 23 cassette to an 11-28.
I'm 185lbs and my rides are no longer than 2 hours. Average 4-500km a month. I got back into cycling last November after a 4 year hiatus.
I will try scraping the paint off the top tube and keeping my back straight. Also spin up the hills, the steeper ones around me I have no choice but to get out of saddle. The higher cadence seems to be helping. Like I say it's only mild discomfort but I just want to ensure I am pedaling correctly so I can get the most out of my knees.