I have been producing various videos with Shotcut for a number of years and have become quite familiar with the software. Overall I have been happy with the results, but learning how to export properly and effectively that fits a certain project is almost an art in itself. I recently completed a project and was shocked when I heard what seemed to be constant clicks, pops and general distortions throughout the video. I was completely at loss as to why this was happening. So I looked the subject up about using aac and ran across this post here: Crackling/Distorted Audio in Exported Video
Exactly my experience. I exported with aac at 48KHz and 100% Quality-based VBR. Unfortunately I cannot go back as the project is already out the door. I am so disappointed in aac I am beside myself. I tried with parallel processing off and on and many other combos and I still had major audio anomalies with aac (Shotcut v22.06.23). So I tried ac3 at 48KHz 100% Quality-based VBR and absolutely crystal clean output in the same exact project with the same exact settings. I have sworn off aac at this point after it pretty much marred my otherwise glitch free project.
I will note my projects usually have multiple video and audio tracks with quite a bit of filter layering. So maybe not the most complex, but certainly not simple projects either. I also will note this problem exists in my export master and is not a YouTube compression issue.