Metro.

All 3 games require you do/don't kill certain people at different levels in order to get the 'true ending'. When I first played I just killed anything that moved, but then found out the consequences of doing so. Honestly it improved my game experience so much more when I had to carefully consider each action.

this one reminds me of Farcry 4. The one with Pagan Min.

if you just stay and be a good boy, you get a free trip to where you really wanted to go.

It's easy to not do this because maybe the welcoming committee is not around anybody's standards.

Elder Scrolls Daggerfall was surely the peek of this, you get a letter at the start telling you to meet a woman in a bar on a set date - turn up too early and she won't be there, but if you mess around on sidequests and don't have enough time to travel there so are late then she'll leave and the main quest never really happens.

There were a million other ways to lock your ability to progress but I always remember that, I don't know if it was possible to get back on track but I don't think so, I probably played a thousand hours before I did a run where I even started the main quest

Final Fantasy Legend for the og Gameboy. I remember getting pretty far in the tower and there was some weapon or item you had to have to pass or beat something and I missed getting it and couldn't progress and never played it again.

The Ooze. My memory on this is fuzzy but on genetics lab part 2, there is a room you can enter that has a checkpoint. If you enter the room then you're locked inside and if you collect the checkpoint and die, you will respawn back into the room and your only option is to lose all your lives or reset the game. I remember getting really pissed off finding this when I was a kid because I spent days trying to beat the game and I had a really good run up until that moment.

I guess this is tangentially related. RDR2 had the full ending for Author and then kept going. I didn't care what happened beyond that so I never finished the epilogue.