I had the same experience with Hokas. Developed pain in the front of my knee from wearing them.
Front of knees (distal to patella more like insertion of quad on fibula) felt weird at the start of runs, but feeling would go away after first quarter mile. Did not have this pain running in any other shoes (Pegasus, pearl izumi, brooks Cascadia)
I only ran easy runs in Clifton 3 and Challenger ATR 4 maybe 4-6miles 3 days a week.
I should have paid more attention because the knee pain has escalated and is mow there all the time.
Stopped wearing the Hokas.
I believe the problem for me with Hokas is lack of forefoot flexibility. You are fully dependent on the shoe and its midsole geometry tapering for toe off.
Hoka has two types of meta-rocker midsole designs.
Hoka late stage meta-rocker midsole did not work at all for me at all (I am a mid/forefoot striker and could not run much faster than 7 flat mile pace in the Stinson)
The early meta-rocker midsole (like on Clifton and Challenger ATR) was better, but not great.
Problem with Hoka shoes is that not everyone can adapt to their midsole designs.