I'm not a plumber - so take this strictly as a guess...
The water flow in your pipes should be sufficiently strong to move any air that collects in the pipes out of the system with no problem.
I suspect that you are pulling some air into the system somewhere. Most likely this is happening on the suction side of your pump.
I would suspect a connection made somewhere in the plumbing coming from your skimmers or main drain.
However you say it's only in 2 of your 3 returns. Are you sure there are no bubble at all in the 3rd return?
I just can't imagine that the pressure and speed of the water won't clear any standing air in the pipe. I truly suspect you have a fitting that isn't sealing well somewhere on the suction side.
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