Paper is a technology. This systemic social problem around paper has the quirks that it does because paper has limitations (you can't add highlights and margin notes after you've given it to somebody else).
If we stop replicating those limitations, it's not unreasonable to expect that the social problem will change also.
I don't think the answer is search engines in the traditional sense, but we probably do need something that knows how to search. If whatever we use to view research were to display warnings wherever a retracted citation was viewed (or whenever one the citations' citations were retracted...), similarly to how we display SSL certificate expiry warnings in a browser, I think that would create a dampening effect on the momentum that a retracted paper can have.
"Retracted" probably isn't the only color we'd want here. "Replicated" might be another. My point is that summoning up-to-date metadata on a something published last year should just be the default view mode, not something you have to ask a grad student to go do.
Knowledge graphs, not dead trees.