The one instance of conflict we've seen since "Arena" was in The Gorn Crisis, but that was with a militant faction that assassinated the sitting regime and was then defeated by Picard. If anything, the Gorn are indebted to the Federation for that.
And I belive that incident was used as background in Gateways: Doors Into Chaos, which showed the two powers working together during the Gateways Crisis.
The incident is also referred to in Losing the Peace
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