United felt aggrieved over the manner of John Terry's 77th minute winner for the hosts.
Phelan told BBC Sport: "I know the manager talks about referees but I think he has a point at times. He has to make these points in order to try and improve the standard.
"The referee obviously gave the off-side decision, the linesman's there, he should see it, (he) didn't do it correctly from what we saw but you have to live with these things in football."
He added: "First and foremost we didn't really think it was a free-kick. We though Darren) Fletcher was committed to the tackle, he won the ball and Ashley Cole was getting out of the way of it really. But on the actual free-kick itself; the delivery of the free-kick, we felt that there was an infringement there against Wes Brown but the referee wasn't in a very good position to see it.
"He should have been in a better position but we should have defender it better and we didn't and we paid the price."