Without logs, which would include which videos, no one can comment further.
I think I have used both MP4 and MKV, and YouTube videos seem to remux fine for me even with SRT.
Or just recently I started doing save as external SRT, and then if unwanted or unneeded, the SRT file can just be deleted.
If not happy with SF Google free YouTube downloaders, there are thousands.
I have several, and between them, there’s never an issue with any YT video I try to download.
There can always be those days YT decides to again make changes to stop downloaders, but using the right combination of downloaders, it’s a very short time, and they can be downloaded again.
Or if people want to pay, there are hundreds of paid YT downloaders; there are even extensions for Firefox that download YT videos. So it can be done right from the browser.
YouTube’s main agenda is to stop anyone from downloading their precious videos due to ‘loss’ of ad revenue, lol.
And it will put a limit on how long a downloader can work before an update is again needed.
It lately seems YT almost daily makes changes.
ADDED:
This, I think, is no longer a valid post.
At best, wait till 7015 comes, and then if there are still issues, make a new post. You MUST post, including a log.