Where were they corning them? It's important with clutter that there's at least an avenue in and out - a piece of clutter pushed up against a wall with no outlet is how they get cornered.
This is a layout of the clutter in my run. Note that I leave spaces around all the objects, so birds can run all the way around (and on top of/under) each object.
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Some pecking is to be expected. I don't consider it an issue as long as no real damage is being done, and as long as the chicks can get away (hence no cornering) and aren't being constantly pursued. Chickens have around a 5-6' personal bubble if there's nothing to break line of sight, so as long as chicks can get further away from the adults than that, they should stop pursuit, which is what you want to see.