I’ve had invalid spanning tree (protocol typically used to prevent loops in networks) packets cause a trunk link to flap as the invalid packet made the switch think its only trunk link (the link to the rest of the network) was part of a loop and shut it down. When the link went down, it could no longer get the bad packets, so after a delay it would enable the trunk again and get the invalid packets again.

I have a very low opinion of STP. I'm also not a fan of the fad to have very flat networks where there are very few routers and instead everything is switches in one gigantic subnet. Packet storms are notoriously difficult to track down on big networks.

That's not a very radical opinion in network engineering circles. No one ever liked it due to it's non forwarding links for loop prevention but it was good enough to work until we discovered it's successor.

Which is?

Impossible, unfortunately, or we wouldn't need STP.

> and moving all redundancy to layer 3 and routing protocols.

Not always possible either, sadly. Works well for new deployments, can difficult to retrofit into older deployments depending on the scale and applications involved.