Cowan felt that the official’s handling of the game 'bordered on incompetence', with eight players – five from the Bucks – receiving yellow cards.
However, it was the awarding of a 56th-minute penalty for alleged manhandling from a corner by Billy Sass-Davies that infuriated Cowan.
“We’ve looked at it, and welcome anyone to look at it and think that it’s a penalty," he said.
"Billy Sass-Davies is absolutely distraught. The referee said he saw the player’s shoulder blade come out of his shirt, which is farcical, a crazy, crazy decision. It just didn’t happen.”
To add insult to Cowan’s sense of injury, referee Sykes turned down three Bucks claims for penalties, one of which looked as much of a foul as the one by Sass-Davies.
Cowan added: “The one on Theo (Streete), it’s a shocking decision. Their lad had two hands on Theo and pushed him to the ground.
"The one on Chris Lait he’s gone down too easily, and I think Laity’s confirmed that himself, but then there’s another on Matty Stenson or Aaron Williams, it’s a blatant penalty.
“It’s consistency; if you don’t give their one, then don’t give ours. But our two were more penalties then their one. Even the Boston players were looking around surprised, even the lad who’s been fouled (Luke Shiels) is unsure of what’s going on.”
The penalty awarded against the Bucks gave Boston’s Jordan Thewlis the chance to put his side head, having equalised just four minutes earlier when the Bucks Zak Lilly was down injured. Thewlis added to those two quick blows with a header on 62 minutes to complete a 10-minute hat-trick.
Although Cowan felt aggrieved, he did also recognise his team hadn’t performed as he’d have liked.
“We have to take responsibility," he added. "We had numerous chances that we really should be converting, and we need to be defending better.
"Boston opened us up too much, and we opened them up too much, which is great for a neutral, but not if you’re a football manager.”