Ive run into a bunch of these myself and there are actually some pretty reliable fixes that work most of the time. First off, grab that 1.0.2 patch if you havent already, it sorts out most of the nasty stuff in missions like On the Edge and A Minor Incident which were giving everyone headaches for a while. Something that really helped me was just verifying the game files through Steam - just right click the game, hit Properties then Local Files and verify everything, fixes a ton of weird issues that pop up.

When youre actually stuck in a mission, try loading up a save from before things went wrong instead of using Continue. Trust me on this one, keeping multiple saves has saved me more times than I can count especially with those tricky missions like Visions of Truth. If youre still having trouble, dropping the texture quality down temporarily usually gets things moving again, and while youre at it maybe bump up your shader cache in the Nvidia settings to about 10GB, worked like a charm for me.

One thing I learned the hard way, if youre stuck in missions like All That is Left at the Chemical Plant, check out the forums real quick, theres usually someone whos found a workaround or the devs have posted something helpful. They've actually fixed hundreds of issues since launch, and theyre still going strong with patches for those pesky A-Life systems. Just remember to report anything really weird you find through their support hub, helps everyone in the long run.