I decided to do some testing. I record MP4 using Bandicam, Mirilis Action and OBS; all have same problem. But when I change recording to AVI, no frame freeze anymore.
Since I do have Camtasia installed, I tried to render some of my MP4 files and did not encounter the same problem.
So it’s safe to assume Shotcut is not really compatible with MP4.
It works fine with nearly all MP4 files I have, but variable frame rate is not supported, and many of the things you mention are creating variable frame rate by default. Also, a very long or open GOP in encode settings can cause a problem. If you encounter such a problem, you can use Properties > Convert, and Shotcut will replace the clip in your project when it is done converting.