"Penalties, whether they're in the scrum or over-competing at rucks is quite daft at some stages, " he said.
BBC: Wales indiscipline daft says Lions centre Jamie Roberts
He has to be first in to rucks on the first phase and his colleagues need to back up well in the phases that follow.
"There is a growing concern...about the conduct of players when entering rucks and mauls...which is considered dangerous, " David Carrigy of the IRB said in the memo.
The move brought its reward as Williams twice broke through from the base of rucks to create the momentum that ended with Bowe going over at the corner.
Matt Banahan's power almost got him over for the first try, however two rucks later Barkley stepped inside prop Kerry Jones to touch down - England international Barkley converting to make it 10-0.
Instead, they responded emphatically as Harinordoquy picked up and burst through a skipper Ryan Jones's poor attempt at a tackle to set up the series of rucks that ended with Thierry Dusautoir touching down.
It took too many Scarlets tacklers to stop a series of driving rucks - Collins just repulsed - and when Januarie and then Biggar spread the ball there were too few defenders out wide.
The crux of it is that if you are on the front foot, attacking well, getting over the gain line and cleaning out rucks, you don't have an issue - the breakdown takes care of itself.
Failure to keep the visitors at bay in crucial rucks in the Wales 22 allowed South Africa to hit Wales on turnover ball, catching Gatland's side without the defensive organisation that had impressed in the first quarter.
With both sides falling foul of referee Rob Debney and conceding a stream of penalties at rucks and scrums the match was a stop-go, error-strewn affair from the fifth minute front-row flare-up which handed Cipriani his opening penalty.
But despite being totally outplayed for the first 40 minutes in Edinburgh they roused themselves after the break and the dominance of their pack in the scrum and at rucks enabled them to grind down their hosts and claim victory.
"I thought in the first half in particular when we made breaks with quick ball there were bodies lingering at the back of rucks and the ball didn't come out, it got turned over or whatever and that's the frustrating thing, there were chances there, " he insisted.
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