The Londoners fell behind early to a superb strike from Ryan Gravenberch, but they responded positively as Enzo Fernandez levelled the score in the 35th minute with a free-kick .
The visitors continued to threaten after the break, with Cole Palmer seeing a goal ruled out for offside following a VAR review.
McFarlane admitted fine margins ultimately denied his side a memorable victory.
“It was a really good performance,” said McFarlane.
“It could have gone either way, really, at certain moments in that game. Probably, being a little bit biased, we could have won the game. We had some good moments.
“I remember Enzo's chance in the first half, Cucurella getting into some really good areas, crossing areas, another marginal offside, a penalty that I thought - and I know it's a tough job for officials - but I think that's a clear penalty. So arguably we could have come away with three points.”