The referee had deemed centreback Milne to have brought down Bay-born midfielder Andy Bevin in the 18m box.
Angell again came under scrutiny when Waugh flashed a yellow card at vice-captain Cory Chettleburgh for a strong challenge in front of the dugout.
"Our view was that it was a hard tackle but a fair one and not worthy of a card," Milne said, not privy to what Angell had said because he was focused on what was transpiring on the field.
Needless to say, fourth official Robert Fleetham thought he had issued enough warnings to Angell to banish him from the sidelines to the stands.
"It was really frustrating for us because, I think, as a loud coach, it has put him in situations where the ref's making his decisions quickly rather than taking a breath and thinking about it," Milne said.
It was hard for him to elaborate because he had not heard Angell's heated exchanges with the officials.
That wasn't the end of it. Angell was then spotted interacting with players after his expulsion behind the stands.
"We didn't have an assistant coach so when you've got to make substitutions, you put them on a piece of paper and Brett had them all in his pocket, so one of the players had to run to him to grab it so we could make substitutions," Milne explained, revealing Bay United took the bare minimum on away matches with a physiotherapist so assistant coach Jamie Dunning was left at home.
"We can't have too many support staff with us because we're only allowed so many people on a flight."
In his coach's defence, the captain said it would not have occurred to Angell the specifics pertaining to the technicalities of the banishment when the coach saw his bench players warming up.
"Things got out of hand again because the ref told me he wasn't allowed to have any communication with the players.
"We got another warning at that point. He said he would disallow us - no default us, I suppose, would have been the word."
Milne had his reservations about whether the statutes of the game gave Waugh the power to carry out the threat.
Angell, he said, would be a spectator in their round 13 encounter against Tasman United at Memorial Park, Palmerston North, this Sunday in a 1pm kick off with Dunning assuming the mantle of coach.
Last summer, Angell found himself in a similar predicament at Park Island, Napier, when fourth official Anthony O'Riley and referee John Rowbury relegated him to the stands in a match against Hamilton Wanderers Soccer Club.
The coach had expressed bewilderment, insisting he was merely pointing out the ref's inconsistencies on the park and hadn't resorted to abusive language or any other offence to warrant a sending off.
... and now for the match report.
Bay striker Saul Halpin drew first blood in the fourth minute from a penalty kick after Taylor Schrijvers' mistimed tackle ground striker Angus Kilkolly in an act no one seemed to be disputing.
However, the lead didn't last long after Wellington striker Ben Harris equalised 1-all in the 12th minute despite goalkeeper Joshua Hill making a superb save from a cornerkick but his defenders failed to clear the ball as Harris turned and pounced on the ball.
Milne said Bay United played intelligently into a stiff wind, keeping the ball on the deck and counterattacking.
From that sort of temperament wing back Fergus Neil made ground on the right flank to cross the ball to the top of the 18m box for Halpin in the 24th minute to reclaim the lead 2-1 and show why he's Bay's top scorer.
Nevertheless, Wellington weren't done as Jackson destroyed Bay souls with an equaliser, 2-2, a minute into added time before the break.
"We slipped up. It was a bad time with a little lapse in the back from a long ball where we didn't clean up enough," said Milne.
He disputed the 3-2 lead from Jackson's spot kick on the grounds that he didn't foul former Napier City Rovers player Bevin.
"I thought that he went down. He got played into the box and I was just holding my space and he goes to the ground.
"We were probably touching each other but I didn't foul him."
Bay substitute striker Facundo Barbero ensured the points were shared with a goal in the 85th minute after the Argentine made good a Chettleburgh cornerkick.
"We had chances to win the game and we would have liked to but the way things were going in the second half it's probably good just to get a point," said Milne bemoaning the halftime lapse and then having to chase the controversial penalty kick.
He said Bay United had beaten Wellington twice on their soil - in the semifinal two seasons ago and in pool play last season.
"Because of their style of play they have done well historically but we were definitely going down there to get the three points so it does feel like a loss."
Milne said his troops felt they were still in the hunt and determined to make the playoffs.
In another stalemate, a gritty 10-men Canterbury United held powerhouses Auckland City to a 2-all draw in Christchurch.
In Auckland, Eastern Suburbs came from a goal down to overwhelm Hamilton Wanderers 3-1 at Bill McKinlay Park.
Waitakere United, who beat Southern United 3-1 at Mosgiel on Saturday, are the new premiership leaders although Auckland have played two fewer games in second place.
Bay United remained in fifth place.
In a rain-delayed match at Nelson, Tasman United 1 scrambled to a 1-all draw against Wellington Phoenix U20s who had under utilised A-League striker Hamish Watson extracting first blood in the 33rd minute.