Did false colors create diplomatic consequences?

Were there diplomatic consequences for warships using another country's flag as a ruse?

Usually little, because intent was difficult to prove; in Ogle's case the Portuguese flag and ship-handling plainly suggest a planned deception.

A neutral government could be told that its flag had been misidentified, making hostile intent difficult to prove. Portugal was also unlikely to press the issue when the target was a pirate rather than a Portuguese vessel. The more revealing point is operational: Swallow already carried the flag and performed a convincing merchantman's turn with a deliberately small-looking working party. Those details indicate that Ogle's disguise was prepared and rehearsed rather than improvised by accident.