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Apart from what has already been mentioned, stuff also gets copyright-struck. Sometimes for ridiculously minor infractions. Sometimes for no real infraction at all.

Additionally, there are the vague and ever-changing terms of service.

Also, people sometimes take stuff down themselves. Take the JRE, for a recent and rather prominent example.

Happens to me often. I don't think it even tells you what videos are gone. I know I've seen channels say they removed a video themselves because it didn't do well with views so they wanted to re-tweak it in the hope it lands better.

Cody's Lab had a video about refining metal ores removed, as one example.

People remove and re-upload (or not) their videos sometimes, so if you could even find it that'd be an annoying extra step.